Skip to main content
SpringerLink
Log in
Book cover

Systems Biology pp 65–124Cite as

Information—its Role and Meaning in Organisms

  • Chapter
  • First Online:

  • 2066 Accesses

Abstract

Information is necessary in regulatory mechanisms which maintain a steady state of activity in individual cells as well as the whole organism. This state corresponds to a genetically encoded program. Without regulation biological processes would become progressively more and more chaotic. In living cells the primary source of information is genetic material. Studying the role of information in biology involves signaling (i.e. spatial and temporal transfer of information) and storage (preservation of information).

Regarding the role of the genome we can distinguish three specific aspects of biological processes: steady-state genetics, which ensure cell-level and body homeostasis; genetics of development, which controls cell differentiation and genesis of the organism; and evolutionary genetics, which drives speciation. A systemic approach to these phenomena must account for the quantitative and qualitative properties of information, explaining that the former are associated with receptor proteins while the latter correspond to biological effectors.

The ever growing demand for information, coupled with limited storage capacities, has resulted in a number of strategies for minimizing the quantity of the encoded information that must be preserved by living cells. In addition to combinatorial approaches based on noncontiguous genes structure, self-organization plays an important role in cellular machinery. Nonspecific interactions with the environment give rise to coherent structures despite the lack of any overt information store. These mechanisms, honed by evolution and ubiquitous in living organisms, reduce the need to directly encode large quantities of data by adopting a systemic approach to information management. Our work represents an attempt to employ the similar mechanisms in the teaching process.

Information determines the function of regulatory mechanisms by reducing the entropy.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Alejster P, Jurkowski W, Roterman I (2012) Structural information involved in the interpretation of the stepwise protein folding process. In: Roterman-Konieczna I (ed) Protein folding in Silico. Woodhead Publishing, Oxford, pp 39–54

    Chapter  Google Scholar 

  • Bryliński M, Konieczny L, Czerwonko P, Jurkowski W, Roterman I (2005) Early-stage folding in proteins (in silico)—Sequence-to-structure relation. Journal of Biomedicine and Biotechnology 2:65–79

    Google Scholar 

  • Bryliński M, Konieczny L, Kononowicz A, Roterman I (2008) Conservative secondary structure motifs already present in early-stage folding (in silico) as fund in serpines family. J. Theoretical Biology 251:275–285,

    Article  Google Scholar 

  • Bryliński M, Jurkowski W, Konieczny L, Roterman I (2004) Early stage of protein folding simulation. Bioinformatics. 20, 199–205

    Article  PubMed  Google Scholar 

  • Jurkowski W, Wiśniowski Z, Konieczny L, Roterman I (2004) The conformational sub-space in simulation of early-stage protein folding Proteins. Structure, function and bioinformatics. 55:115–127

    Google Scholar 

  • Jurkowski W, Baster Z, Dułak D, Roterman-Konieczna I (2012) The aarly-stage intermediate. In: Roterman-Konieczna I (ed) Protein folding In Silico. Woodhead Publishing, Oxford, pp 1–20

    Chapter  Google Scholar 

  • Leluk J, Konieczny L, Roterman I (2003) Search for structural similarity in proteins. Bioinformatics 19:117–124

    Article  PubMed  CAS  Google Scholar 

  • Roterman I (1995) Modelling the optimal simulation path in the peptide chain folding—studies based on geometry of alanine heptapeptide. J. Theoretical Biology 177:283–288

    Article  CAS  Google Scholar 

  • Roterman I (1995) The geometrical analysis of structural peptide backbone structure and its local deformations. Biochimie 77:204–252

    Article  PubMed  CAS  Google Scholar 

  • Roterman I, Konieczny L (1995) Geometrical analysis of structural changes in immunoglobin domains’ transition from native to molten state. Computers and Chemistry 19:204–216

    Article  Google Scholar 

  • Ashby WR (1958) An introduction to cybernetics. Chapman & hall, London

    Google Scholar 

  • Beatty J, Legewie H (1976) Biofeedback of behavior NATO Conference Series Serie III. Human Factors Plenum Press, New York/London

    Google Scholar 

  • Bernstein HD (2012) All clear for ribosome landing. Nature 492:189–191

    Article  PubMed  CAS  Google Scholar 

  • Bhutani N, Brady JJ, Damian M, Sacco A, Corbel SY, Blau HM (2010) Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature 463:1042–1047

    Article  PubMed  CAS  Google Scholar 

  • Bjorklund S, Kim Y-J (1996) Mediator of transcriptional regulation. TIBS 21:335–337

    PubMed  CAS  Google Scholar 

  • Brennan MD, Cheong R, Levchenko A (2012) How information theory handles cell signaling and uncertainty. Science 338:334–335

    Article  PubMed  CAS  Google Scholar 

  • Brown CE, Lechner T, Howe L, Workman JL (2000) The many HATs of transcription coactivators. TIBS 25:15–19

    PubMed  CAS  Google Scholar 

  • Buchner J (1999) Hsp90 & Co.—a holding for folding. TIBS 24:136–141

    PubMed  CAS  Google Scholar 

  • Bycroft M (2011) Recognition of non-methyl histone marks. Curr Op Struct Biol 21:761–766

    Article  CAS  Google Scholar 

  • Cesare D, Fimia GM, Sassone-Corsi P (1999) Signaling routes to CREM and CREB: plasticity in transcriptional activation. TIBS 24, 281–285

    PubMed  Google Scholar 

  • Chambers I, Silva J, Colby D, Nichols J, Nijmeijer B, Robertson M, Vrana J, Jones K, Grotewold L, Smith A (2007) Nanog safeguards pluripotency and mediates germline development. Nature 450:1230–1234

    Article  PubMed  CAS  Google Scholar 

  • Chin JW (2012) Reprogramming the genetic code. Science 336:428–429

    Article  PubMed  CAS  Google Scholar 

  • Cooper GM (1997) The Cell—a molecular approach. ASM Press, Washington

    Google Scholar 

  • Cramer P, Bushnell DA, Fu J, Gnatt AL, Maier-Davis B, Thompson NE, Burgess RR, Edwards AM, David PR, Korneberg RD (2000) Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288:640–649

    Article  PubMed  CAS  Google Scholar 

  • Dethoff EA, Chugh J, Mustoe AM, Al-Hashimi HM (2012) Functional complexity and regulation through RNA dynamics. Nature 482:322–330

    Article  PubMed  CAS  Google Scholar 

  • Dever TE (1999) Translation initiation: adept at adapting. TIBS 24:398–403

    PubMed  CAS  Google Scholar 

  • Downs JA, Nussenzweig MC, Nussenzweig A (2007) Chromatin dynamics and the preservation of genetic information. Nature 447:951–958

    Article  PubMed  CAS  Google Scholar 

  • Fedoroff NV (2012) Transposable elements, epigenetics and genome evolution. Science 338:758–767

    Article  PubMed  CAS  Google Scholar 

  • Frydman J, Hohfeld J (1997) Chaperones get in touch: the Hip-Hop connection TIBS 22:87–92

    Google Scholar 

  • Garber K (2012) All eyes on RNA. Science 338:1282–1283

    Article  PubMed  CAS  Google Scholar 

  • Gkikopoulos T, Schofield P, Singh V, Pinskaya M, Mellor J, Smolle M, Workman JL, Barton GJ, Owen-Hughes T (2011) A role for Snf2-related nucleosome-splicing enzymes in genome-wide nucleosome organization. Science 333, 1758–1760

    Article  PubMed  CAS  Google Scholar 

  • Graf T, Enver T (2009) Forcing cells to change lineages. Nature, 462, 587–592

    Article  PubMed  CAS  Google Scholar 

  • Gullberg D (2003) The molecules that make muscle. Nature, 424, 138–140

    Article  PubMed  CAS  Google Scholar 

  • Guttman M, Rinn JL (2012) Modular regulatory principles of large non-coding RNAs. Nature 482:339–346

    Article  PubMed  CAS  Google Scholar 

  • Harel D (1987) Algorithmics: the spirit of computing. Addison-Wesley, Reading

    Google Scholar 

  • Kaplan T, Friedman N (2012) Running to stand still. Nature 484:171–172

    Article  PubMed  CAS  Google Scholar 

  • Khorasanizadeh S (2011) Recognition of methylated histone new twists and variations. Curr Op Struct Biol 21:744–749

    Article  CAS  Google Scholar 

  • Kornberg RD (1996) RNA polymerase II transcription control. TIBS 21:325–326

    PubMed  CAS  Google Scholar 

  • Kosak ST, Groudine M (2004) Gene order and dynamic domains. Science 306, 644–650

    Article  PubMed  CAS  Google Scholar 

  • Kueh HY, Mitchison TJ (2009) Structural plasticity in actin and tubulin polymer dynamics. Science 325:960–963

    Article  PubMed  CAS  Google Scholar 

  • de Latil P (1953) La pensée artificielle. Ed. Gallimard, Paris

    Google Scholar 

  • Lee JT (2012) Epigenetic regulation by long noncoding RNAs. Science 338:1435–1439

    Article  PubMed  CAS  Google Scholar 

  • Leschziner AE (2011) Electron microscopy studies on nucleosome remodelers. Curr Op. Struct Biol 21:709–718

    CAS  Google Scholar 

  • Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD (2012) Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature 484:251–255

    Article  PubMed  CAS  Google Scholar 

  • Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O’Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, Evans RM, Ecker JR (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471, 68–73

    Article  PubMed  CAS  Google Scholar 

  • Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J (1999) Molecular cell biology. W. H. Freeman and Company, New York

    Google Scholar 

  • Lombardi PM, Cole KE, Dowling DP, Christianson DW (2011) Structure mechanism and inhibition of histone deacetylases and related metalloenzymes. Curr Op Struct Biol 21:735–743

    Article  CAS  Google Scholar 

  • Lujambio A, Lowe SW (2012) The microcosmos of cancer. Nature 482:347–355

    Article  PubMed  CAS  Google Scholar 

  • Luxton R, Pallister CJ (1999) Clinical biochemistry. Butterworth-Heineman, Oxford

    Google Scholar 

  • Al Mamun AAM, Lombardo M-J, Shee C, Lisewski AM, Gonzalez C, Lin D, Nehring RB, Saint-Ruf C, Gibson JL, Frisch RL, Lichtarge O, Hastings PJ, Rosenberg SM (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338:1344–1348

    Article  PubMed  CAS  Google Scholar 

  • Margueron R, Reinberg D (2011) The polycomb complex PRC2 and its mark in life. Nature 467:343–349

    Article  Google Scholar 

  • Mishra SK, Ammon T, Popowicz GM, Krajewski M, Nagel RJ, Ares M Jr, Holak TA, Jentsch S (2011) Role of ubiquitin-like protein Hub1 in splice-site usage and alternative splicing. Nature 474:173–178

    Article  PubMed  CAS  Google Scholar 

  • Morelli LG, Uriu K, Ares S, Oates AC (2012) Computational approaches to developmental pattering. Science 336:187–191

    Article  PubMed  CAS  Google Scholar 

  • Munsky B, Neuert G, van Oudenaarden A (2012) Using gene expression noise to understand gene regulation. Science 336:183–187

    Article  PubMed  CAS  Google Scholar 

  • Netzer WJ, Hartl FU (1998) Protein folding in the cytosol: chaperonin-dependent and independent mechanism. TIBS 23:68–73

    PubMed  CAS  Google Scholar 

  • Nicholas CR, Kriegstein AR (2010) Cell reprogramming gets direct. Nature 463:1031–1032

    Article  PubMed  CAS  Google Scholar 

  • Pennisi E (2012) Gene duplication’s role in evolution gets richer, more complex. Science 338:316–317

    Article  PubMed  CAS  Google Scholar 

  • Pham P, Bransteitter R, Petruska J, Goodman MF (2003) Progressive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation. Nature 424:103–107

    Article  PubMed  CAS  Google Scholar 

  • Poletajew JA (1964) Empfang der sprachlichen Mittel—Walter de Gruyter

    Google Scholar 

  • Pollard TD, Earnshaw W (2002) Cell biology. Saunders, Philadelphia

    Google Scholar 

  • Przeworski M (2005) Motivating hotspots. Science 310:247–248

    Article  PubMed  CAS  Google Scholar 

  • Richardson A, Landry SJ, Georgopoulos C (1998) The ins and outs of a molecular chaperone machine. TIBS 23:138–143

    PubMed  CAS  Google Scholar 

  • Roeder RG (1996) The role of general initiation factors in transcription by RNA polymerase II. TIBS 21:327–335

    PubMed  CAS  Google Scholar 

  • Schleif R (1985) Genetics & molecular biology. Addison-Wesley Publishing Company, New York

    Google Scholar 

  • Shen K, Arslan S, Akopian D, Ha T, Shan S-o (2012) Activated GTPase movement on an RNA scaffold drives co-translational protein targeting. Nature 492:271–275

    Article  PubMed  CAS  Google Scholar 

  • Sheth R, Marcon L, Bastida MF, Junco M, Quintana L, Dahn R, Kmita M, Sharpe J, Ros MA (2012) Hox genes regulate digit patterning by controlling the wavelength of a Turing-type mechanism. Science 338:1476–1480

    Article  PubMed  CAS  Google Scholar 

  • Simpson JL (2006) Medicine—Blastomeres and stem cells. Nature 444:432–435

    Article  PubMed  CAS  Google Scholar 

  • Srivastava R, Ram BP, Tyle P (1991) Molecular mechanisms of immune regulation. VCH, New York

    Google Scholar 

  • Streyer L (1995) Biochemistry. W.H. Freeman and Company

    Google Scholar 

  • Svejstrup JQ, Vichi P, Egly J-M (1996) The multiple roles of transcription repair factor TFIIH. TIBS 21:346–350

    PubMed  CAS  Google Scholar 

  • LaThangue NA (1994) DRTF1/E2F: an expanding family of heterodimeric transcription factors implicated in cell-cycle control. TIBS 19:108–114

    CAS  Google Scholar 

  • Timsit Y (1999) DNA structure and polymerase fidelity. J Mol Biol 293:835–853

    Article  PubMed  CAS  Google Scholar 

  • Torrence PF (2000) Biomedical chemistry-applying chemical principles to the understanding and treatment of disease. Wiley-Interscience John Wiley & Sons, Inc. Publication, New York

    Google Scholar 

  • Upadhyay AK, Horton JR, Zhang X, Cheng X (2011) Coordinated methyl-lysine erasure: structural and functional linkage of a Jumonji demethylase domain and a reader domain. Curr Op Struct Biol 21:750–760

    Article  CAS  Google Scholar 

  • Vierbuchen T, Ostermeier A, Pang ZP, Kokubu Y, Südhof TC, Wernig M (2010) Direct conversion of fibroblast to functional neurons by defined factors. Nature 463:1035–1041

    Article  PubMed  CAS  Google Scholar 

  • Voet D, Voet JG (1995) Biochemistry. Wiley, New York

    Google Scholar 

  • Wiedenheft B, Sternberg SH, Doudna JA (2012) RNA-guided genetic silencing systems in bacteria and archaea. Nature 482:331–338

    Article  PubMed  CAS  Google Scholar 

  • Wilson EO (1971) The Insect Societies The Belknap Press of Harvard University Press. Cambridge

    Google Scholar 

  • Yonath A (2006) Molecular biology—triggering positive competition. Nature 444:435–436

    Article  PubMed  CAS  Google Scholar 

  • Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, Slukvin II, Thomson JA (2007) Induced pluripotent stem cell lines derived from human somatic cells. Science 318:1917–1922

    Article  PubMed  CAS  Google Scholar 

  • Zheleznova EE, Markham P, Edgar R, Bibi E, Neyfakh AA, Brennan RG (2000) A structure-based mechanism for drug binding by multidrug transporters. TIBS 25:39–43

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Medicinal Chemistry, Jagiellonian University Medical College, Krakow, Poland

    Leszek Konieczny

  2. Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Krakow, Poland

    Irena Roterman-Konieczna & Paweł Spólnik

Authors
  1. Leszek Konieczny
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Irena Roterman-Konieczna
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Paweł Spólnik
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Leszek Konieczny .

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Konieczny, L., Roterman-Konieczna, I., Spólnik, P. (2014). Information—its Role and Meaning in Organisms. In: Systems Biology. Springer, Cham. https://doi.org/10.1007/978-3-319-01336-7_3

Download citation

Publish with us

Policies and ethics

Search

Navigation