BASIC CELL BIOLOGY

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BASIC CELL BIOLOGY. I CHEMISTRY of LIFE. Indriķis Muižnieks. II STRUCTURE OF THE CELL. Tūrs Selga. I CHEMISTRY OF LIFE. Structure of the Biological Sciences. Atomic Structure and the Periodic Table of the Elements.
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BASIC CELL BIOLOGYI CHEMISTRY of LIFEIndriķis MuižnieksII STRUCTURE OF THE CELLTūrs SelgaI CHEMISTRY OF LIFE
  • Structure of the Biological Sciences.
  • Atomic Structure and the Periodic Table of the Elements.
  • Chemical Bonding, Intermolecular Forces. Properties of the Water, Buffer Solutions.
  • Classification of the Organic Compounds, Functional Groups.
  • Biopolymers.
  • Basic Principles of the Metabolism.
  • READING:N.A. Campbell; Biology, Benjamin Cummings Publ., 4-th edition, 1996Unit 1 (pp. 25-103)Chapter 23 (pp. 469 - 479)READING:N.A. Campbell, J.B. Reece andL.G. Mitchell BIOLOGY,Benjamin Cummings Publ., 5-th edition, 1999IntroductionUnit 1 (pp. 20-100)ADDITIONAL READING:
  • B.Rockett & R.Stutton; Chemistry for Biologists, 1996
  • A. Zeeck et al. Chemie für Mediziner, 1992
  • “ Biochemistry” (Zane) discs in the server of the Faculty
  • Internet information
  • Lecture 1STRUCTURE OF THE BIOLOGICAL SCIENCES
  • Structural and functional diversity of Biological Systems
  • Methodology of Biological Research and Teaching
  • The principles of Classification in Biology; Five Kingdoms of Life
  • Lecture 1SCIENCESHUMANITIESSOCIALMEDICALAGRICULTURALENGINEERINGEDUCATIONNATURAL andMATHEMATICSLecture 1NATURAL SCIENCESPHYSICSASTRONOMYCHEMISTRYGEOGRAPHYGEOLOGYBIOLOGY:study of living things and their vital processes.Lecture 1
  • LIFE :
  • the state of a material complex or individual characterized
  • by the capacity to perform certain functional activities,
  • including:
  • metabolism,
  • growth,
  • reproduction,
  • some form of responsiveness,
  • adaptation.
  • Life is further characterized by the presence of complex transformations of organic molecules and by the organization of such molecules into the successively larger units of protoplasm, cells, organs, and organisms.
  • Encyclopaedia Britannica
  • Lecture 1IN A UNIVERSE THAT IS DOMINATED BY INCREASING ENTROPY, LIVING ORGANISMS ARE A CURIOUS ANOMALITY. THE ORGANISATION THAT DISTINGUISHES LIVING ORGANISMS FROM THEIR INNATE SURROUNDINGS RELIES UPON THEIR ABILITY TO EXECUTE VECTORIAL PROCESSES, SUCH AS DIRECTED MOVEMENTS AND THE ASSEMBLY OF MACROMOLECULES AND ORGANELLE SYSTEMS.Roland D. Vale ( TIBS Millenium Issue, M38, Dec. 1999)TELEOLOGY - DOES THE NATURE HAVE PURPOSE ?Lecture 1Structural and functional diversity of biological systems.FUNCTIONSORIGIN OF SPECIESEVOLUTIONINTERACTIONS WITH THE ENVIRONMENTECOLOGYINTERACTIONS WITH COUNTERPARTSPOPULATION BIOLOGYMANTENANCE OF IDENTITYIMMUNOLOGYHEREDITY AND MUTATIONGENETICSFUNCTIONS OF ORGANS AND SYSTEMSPHYSIOLOGYDEVELOPMENTEMBRIOLOGY, DEVELOPMENTAL BIOLOGYMETABOLISMBIOCHEMISTRY, BIOPHYSICSLecture 1Structural and functional diversity of biological systems.STRUCTUREDIVERSITY OF LIFETAXONOMYSPECIESSYSTEMATICSORGANISMSMORPHOLOGYORGANS, SYSTEMSANATOMYTISSUESHISTOLOGYCELLSCYTOLOGY, CELL BIOLOGYMACROMOLECULESMOLECULAR BIOLOGYMOLECULESBIOCHEMISTRY, BIOPHYSICSLecture 1Structural and functional diversity of biological systems.OBJECTSANIMALSZOOLOGYPLANTSBOTANYFUNGIMYCOLOGYUNICELLULAR ORGANISMSPROTISTOLOGYBACTERIABACTERIOLOGYNON-CELLULAR FORMS OF LIFE VIROLOGYOBJECTSLecture 1Branches of BiologyFunctionsEVOL UTIONThe study of the specific structures and functions of defined objects.Plant Anatomy ECO LOGYBacterial geneticsPOPULATION BIOLOGYAnimal PhysiologyIMMUN OLOGYGENE TICSMolecular biology of the VirusesPHYSI OLOGYDEVELOPME NTAL BILOGYBIOCHEMISTRY, BIOPHYSICSVIROLOGYMOLECULAR BIOLOGYBACTERIOLOGYCITOLOGYPROTISTOLOGYHISTOLOGYMICOLOGYANATOMYBOTANYMORPHOLOGYZOOLOGYTAKSONOMYObjectsStructureSPECIALISATIONS OF BIOLOGYLecture 1Branches of BiologyFURTHER SUBDIVISION OF THE BRANCHESBOTANYTrees DendrologyAlgae PhycologyMosses Briology Lichens LichenologyLecture 1Branches of BiologyFURTHER SUBDIVISION OF THE BRANCHESZOOLOGYMammals Mammology Birds OrnithologyReptiles and Herpetologyamphibians Fishes IchtiologyInsects EntomologyMolluscs, snails MalacologyLecture 1Branches of BiologySYNTHETIC BRANCHES OF BIOLOGYMICROBIOLOGYthe use of specific research methods in the studies of viruses, bacteria, microscopic fungi and protistsHYDROBIOLOGYthe study of life in water environmentCELL BIOLOGYsupplementation of the research in cytology with the methods of molecular biology and development biologyLecture 1Branches of BiologyFunctionsVisualisation of the objects and structuresEVOL UTIONMicroscope ECO LOGYPOPULATION BIOLOGYConstruction of self-replicating nucleic acids in vitroIMMUN OLOGYGenetical engineeringGENE TICSPHYSI OLOGYDEVELOPME NTAL BILOGYBiometryData processing and assessmentBIOCHEMISTRY, BIOPHYSICSVIROLOGYMOLECULAR BIOLOGYBACTERIOLOGYCITOLOGYPROTISTOLOGYHISTOLOGYMICOLOGYANATOMYMETHODS OF INVESTIGATIONBOTANYMORPHOLOGYZOOLOGYTAXONOMYStructureObjectsLecture 1Branches of BiologyThe use of the knowledge from other branches of science for the development of biological research.Reflecting sub-branchesBiochemistry, Biophysics, Paleobiology, Zoogeography.Lecture 1Branches of BiologyUse of biological knowledge for the development or establishment of new sub-branches.Projecting sub-branchesSmall projectionsThe application of a knowledge or methods from one branch of Biology into some other field of research.Medical microbiology; Parasitology; Agricultural entomology; Psychophysiology.Large projectionsVersatile application of the Biological knowledge in the other field of science.Biotechnology, Environment Sciences, BiomedicineLecture 1Principles of Studies in BiologyThe Scientific Method
  • Hypothesis
  • Assumption, that can be tested by further investigations
  • Hypothesis tray to explain, provide knowledge, it is not a simple registration of the fact
  • Hypothesis are rooted in the theory or in the experience
  • Hypothesis should be versatile
  • Hypothesis should be assessable
  • Hypothesis can be rejected but never affirmed to completeness
  • Deduction: generation of hypothesis on the basis of theory
  • Lecture 1Principles of Studies in BiologyScientific MethodTheoryClassified knowledge which is attributable under various circumstances, also the system of assumptions, principles and methods of analysis produced to explain and predict definite phenomena or processes. Theory is formed by Induction - systematisation of facts, conclusions, observationsTheory is characterised by itsForce of deduction - capability to create testable hypothesisNothing is as practical as a good theoryLecture 1Principles of Studies in BiologyScientific MethodTHEORYDEDUCTIONINDUCTIONEXPLANATIONCONCLUSION (observation, fact)HYPOTHESISVALIDATIONEXPERIENCELecture 1Principles of Studies in BiologyMethods of Assessment
  • Experiment
  • action which is performed under controlled conditions to prove the correctnes of the assumption or to test the impact of the studied factor
  • Simplification
  • Invasive
  • Controls (+/-)
  • Universal (independence of the place where it is performed)
  • Lecture 1Principles of Studies in BiologyMethods of Assessment
  • Observation
  • Formalised description of the object or phenomenon
  • Complex
  • Non-invasive
  • Camparable versions (differences in context)
  • Unique (dependent on the place where it is performed )
  • Lecture 1The Principles of Studies in BiologyMethodological ApproachesReductionisma view that asserts that entities of a given kind are collections or combinations of entities of a simpler or more basic kind or that expressions denoting such entities are definable in terms of expressions denoting the more basic entities. Thus, the ideas that physical bodies are collections of atoms or that thoughts are combinations of sense impressions are forms of reductionismLecture 1The Principles of Studies in BiologyMethodological ApproachesHolism the theory that the determining factors in biology are its irreducible wholes.Emergent propertiesat each successive level of organization, qualities emerge that cannot be anticipated by the components and that confer an added dimension to each hierarchical level in the biological world.Lecture 1The Principles of Studies in BiologyDidactic ApproachesFactologyAcquisition and memorisation of the specific data which characterise the given object or system. ConceptualismDevelopment of understanding about the structural, functional and regulatory principles of the given object or system.Lecture 1The Principles of Studies in BiologyDidactic ApproachesOverlappingNew knowledge is gained on the basis of the existing one, before the development of the thesaurus its contents should be actualised.EvolutionConsequtive acquisition of the theories and skills, movmet from the non-complicated to complex, from general to peculiar and furthen on to synthesis. Lecture 1The Principles of Studies in BiologyFunctionsEVOL UTION ECO LOGYPOPULATION BIOLOGYIMMUN OLOGYGENE TICSPHYSI OLOGYDEVELOPME NTAL BILOGYBIOCHEMISTRY, BIOPHYSICSVIROLOGYMOLECULAR BIOLOGYBACTERIOLOGYCITOLOGYPROTISTOLOGYHISTOLOGYCHEMISTRYPHYSICSMICOLOGYANATOMYBOTANYMORPHOLOGYZOOLOGYTAKSONOMYStructureObjectsLecture 1The Principles of Studies in BiologyLecture 1The principles of Classification in BiologyThe Development of the Classification Approximates the History of BiologyTaxonomy– (Classification in Biology, Systematics) the branch of Biology considering the phylogeny of living and extinct species. Greek taxis (arrangement) and nomos (law). Taxonomy deals with the establishment of a hierarchical system of categories on the basis of presumed natural relationships among organisms.Natural taxonomyArtificial taxonomyLecture 1The principles of Classification in BiologyLecture 1The principles of Classification in BiologyLecture 1The principles of Classification in BiologyLecture 1The principles of Classification in BiologyLecture 1The principles of Classification in BiologyAristotles(384.-322. BC)Scala Naturae, Historia AnimalumGods, Humans, Mammals, Birds, Fishes, Insects, Plants, Minerals.Lecture 1The principles of Classification in BiologyCarl Linneus (1707-1778),Species Plantarum (1753) Systema Naturae (1758)Binary nomenclatureLecture 1The principles of Classification in BiologyJean Lamarck(1744-1829),Flore Francaise (1778.), Historie Naturelle des Animaux sans Vertebres (1815.-1822.). Inheritance of obtained qualities (1801. –1809.).“Biology” -1802.Lecture 1The principles of Classification in BiologyGeorge Cuvier(1769.-1832.),Animal classification: Vertebrates; Insects, Worms. Paleontology, Theory of Catastrophies.Lecture 1The principles of Classification in BiologyDarwin “On the Origin of Species”: … classification will become genealogyCharles Darwin(1809. - 1882.)On the Origin of Species by Means of Natural Selection (1859.)The Descent of Man, and Selection in Relation to Sex (1871.)Lecture 1The principles of Classification in BiologyErnst Mayr(1904.-)Synthetic theory of evolution,Methods and Principles of Systemic Zoology Animal Species and Evolution (1963.)The definition of species according to E. Meyr: “groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups.”Lecture 1The principles of Classification in BiologyTHE MAIN SCHOOLS OF TAXONOMYPHENETICCLADISTICMOLECULAREVOLUTIONARYLecture 1The principles of Classification in BiologyPHENETIC TAXONOMYAlso called numeric or numeral taxonomy.The classification is based on general similarity of morphological or genetic traits.Lecture 1The principles of Classification in BiologyPHENETIC TAXONOMY1) Voges-Proskauer (VP); 2) Nitrate(N); 3) Phe-deaminase (PD); 4) H2S; 5) indole (I); 6) Orithine decarboxylase (OD); 7) Lisine decarboxylase (LD); 8) Malonic acid (M); 9) Urea (U); 10) Esculine (E); 11) ONPG 12) Arabinose (ARAB); 13) Adonitol (ADON); 14) Inosite (INOS); 15) Sorbite (SORB)Identification of Enterobacteriaceae within four hours. Groups of three reactions.Codes: 1. positive, 4; 2. positive, 2; 3. positive, 1; no positives, 0.Escherichia coli code: 23430Lecture 1The principles of Classification in BiologyCLADISTIC TAXONOMYClade (angl.) – group formed by a common ancestor and its offspring. Existing organisms are thought as the end-points of branches. The structure of branching is determined by pattern of commonly acquired features (sinapomorphies)The principles of parsimony (economy) and consensus (agreement);Plesiomorphic (ancient) un apomorphic (new) traitsLecture 1The principles of Classification in BiologyMOLECULAR TAXONOMYmolecular taxonomy deals with structures of genomes (DNA) or with the products of genome expression - RNA or protein.DNA analysis: sequencing, hybridisation, restriction fragment comparison.Sequencing of the ribosomal RNA.Analysis of the primary structure of proteins.Lecture 1The principles of Classification in BiologyThe hypothesis of the molecular clock assumes that the changes in the biomolecules accumulate slowly, but with a constant speed. If the speed is constant, then the number of differences in two analogous molecules in different organisms is proportional to the time which has elapsed since these organisms have had a common ancestor.The changes in the structure of molecules record the process of evolution.Lecture 1The principles of Classification in BiologyEVOLUTIONARY TAXONOMYDarwin “On the Origin of Species”: … classification will become genealogyUses and combines several approaches to obtain the classification which corresponds to the natural history of the organisms and maximise the mutual similarity of the organisms included into one taxonomic category. Classification takes place through iterative grouping and regrouping of organisms according to various analytical approaches and the paleontologic record. Convergence, analogy and homology of traits.Lecture 1The principles of Classification in BiologyFIVE KINGDOMS OF LIFENON-CELLULAR FORMS OF LIFELecture 1The principles of Classification in BiologyTHREE DOMAINS OF LIFE
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