BASIC CELL BIOLOGY

1. BASIC CELL BIOLOGY I CHEMISTRY of LIFE Indriķis Muižnieks II STRUCTURE OF THE CELL Tūrs Selga

2. I 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.

3. READING: N.A. Campbell; Biology, Benjamin Cummings Publ., 4-th edition, 1996 Unit 1 (pp. 25-103) Chapter 23 (pp. 469 - 479)

4. READING: N.A. Campbell, J.B. Reece and L.G. Mitchell BIOLOGY, Benjamin Cummings Publ., 5-th edition, 1999 Introduction Unit 1 (pp. 20-100)

5. 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

6. Lecture 1 STRUCTURE 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

7. Lecture 1 SCIENCES HUMANITIES SOCIAL MEDICAL AGRICULTURAL ENGINEERING EDUCATION NATURAL and MATHEMATICS

8. Lecture 1 NATURAL SCIENCES PHYSICS ASTRONOMY CHEMISTRY GEOGRAPHY GEOLOGY BIOLOGY: study of living things and their vital processes.

9. 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

10. Lecture 1 IN 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 ?

11. Lecture 1 Structural and functional diversity of biological systems. FUNCTIONS ORIGIN OF SPECIES EVOLUTION INTERACTIONS WITH THE ENVIRONMENT ECOLOGY INTERACTIONS WITH COUNTERPARTS POPULATION BIOLOGY MANTENANCE OF IDENTITY IMMUNOLOGY HEREDITY AND MUTATION GENETICS FUNCTIONS OF ORGANS AND SYSTEMS PHYSIOLOGY DEVELOPMENT EMBRIOLOGY, DEVELOPMENTAL BIOLOGY METABOLISM BIOCHEMISTRY, BIOPHYSICS

12. Lecture 1 Structural and functional diversity of biological systems. STRUCTURE DIVERSITY OF LIFE TAXONOMY SPECIES SYSTEMATICS ORGANISMS MORPHOLOGY ORGANS, SYSTEMS ANATOMY TISSUES HISTOLOGY CELLS CYTOLOGY, CELL BIOLOGY MACROMOLECULES MOLECULAR BIOLOGY MOLECULES BIOCHEMISTRY, BIOPHYSICS

13. Lecture 1 Structural and functional diversity of biological systems. OBJECTS ANIMALS ZOOLOGY PLANTS BOTANY FUNGI MYCOLOGY UNICELLULAR ORGANISMS PROTISTOLOGY BACTERIA BACTERIOLOGY NON-CELLULAR FORMS OF LIFE VIROLOGY OBJECTS

14. Lecture 1 Branches of Biology Functions EVOL UTION The study of the specific structures and functions of defined objects. Plant Anatomy ECO LOGY Bacterial genetics POPULATION BIOLOGY Animal Physiology IMMUN OLOGY GENE TICS Molecular biology of the Viruses PHYSI OLOGY DEVELOPME NTAL BILOGY BIOCHEMISTRY, BIOPHYSICS VIROLOGY MOLECULAR BIOLOGY BACTERIOLOGY CITOLOGY PROTISTOLOGY HISTOLOGY MICOLOGY ANATOMY BOTANY MORPHOLOGY ZOOLOGY TAKSONOMY Objects Structure SPECIALISATIONS OF BIOLOGY

15. Lecture 1 Branches of Biology FURTHER SUBDIVISION OF THE BRANCHES BOTANY Trees Dendrology Algae Phycology Mosses Briology Lichens Lichenology

16. Lecture 1 Branches of Biology FURTHER SUBDIVISION OF THE BRANCHES ZOOLOGY Mammals Mammology Birds Ornithology Reptiles and Herpetology amphibians Fishes Ichtiology Insects Entomology Molluscs, snails Malacology

17. Lecture 1 Branches of Biology SYNTHETIC BRANCHES OF BIOLOGY MICROBIOLOGY the use of specific research methods in the studies of viruses, bacteria, microscopic fungi and protists HYDROBIOLOGY the study of life in water environment CELL BIOLOGY supplementation of the research in cytology with the methods of molecular biology and development biology

18. Lecture 1 Branches of Biology Functions Visualisation of the objects and structures EVOL UTION Microscope ECO LOGY POPULATION BIOLOGY Construction of self-replicating nucleic acids in vitro IMMUN OLOGY Genetical engineering GENE TICS PHYSI OLOGY DEVELOPME NTAL BILOGY Biometry Data processing and assessment BIOCHEMISTRY, BIOPHYSICS VIROLOGY MOLECULAR BIOLOGY BACTERIOLOGY CITOLOGY PROTISTOLOGY HISTOLOGY MICOLOGY ANATOMY METHODS OF INVESTIGATION BOTANY MORPHOLOGY ZOOLOGY TAXONOMY Structure Objects

19. Lecture 1 Branches of Biology The use of the knowledge from other branches of science for the development of biological research. Reflecting sub-branches Biochemistry, Biophysics, Paleobiology, Zoogeography.

20. Lecture 1 Branches of Biology Use of biological knowledge for the development or establishment of new sub-branches. Projecting sub-branches Small projections The application of a knowledge or methods from one branch of Biology into some other field of research. Medical microbiology; Parasitology; Agricultural entomology; Psychophysiology. Large projections Versatile application of the Biological knowledge in the other field of science. Biotechnology, Environment Sciences, Biomedicine

21. Lecture 1 Principles of Studies in Biology The 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

22. Lecture 1 Principles of Studies in Biology Scientific Method Theory Classified 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, observations Theory is characterised by its Force of deduction - capability to create testable hypothesis Nothing is as practical as a good theory

23. Lecture 1 Principles of Studies in Biology Scientific Method THEORY DEDUCTION INDUCTION EXPLANATION CONCLUSION (observation, fact) HYPOTHESIS VALIDATION EXPERIENCE

24. Lecture 1 Principles of Studies in Biology Methods 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)

25. Lecture 1 Principles of Studies in Biology Methods 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 )

26. Lecture 1 The Principles of Studies in Biology Methodological Approaches Reductionism a 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 reductionism

27. Lecture 1 The Principles of Studies in Biology Methodological Approaches Holism the theory that the determining factors in biology are its irreducible wholes. Emergent properties at 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.

28. Lecture 1 The Principles of Studies in Biology Didactic Approaches Factology Acquisition and memorisation of the specific data which characterise the given object or system. Conceptualism Development of understanding about the structural, functional and regulatory principles of the given object or system.

29. Lecture 1 The Principles of Studies in Biology Didactic Approaches Overlapping New knowledge is gained on the basis of the existing one, before the development of the thesaurus its contents should be actualised. Evolution Consequtive acquisition of the theories and skills, movmet from the non-complicated to complex, from general to peculiar and furthen on to synthesis.

30. Lecture 1 The Principles of Studies in Biology Functions EVOL UTION ECO LOGY POPULATION BIOLOGY IMMUN OLOGY GENE TICS PHYSI OLOGY DEVELOPME NTAL BILOGY BIOCHEMISTRY, BIOPHYSICS VIROLOGY MOLECULAR BIOLOGY BACTERIOLOGY CITOLOGY PROTISTOLOGY HISTOLOGY CHEMISTRY PHYSICS MICOLOGY ANATOMY BOTANY MORPHOLOGY ZOOLOGY TAKSONOMY Structure Objects

31. Lecture 1 The Principles of Studies in Biology

32. Lecture 1 The principles of Classification in Biology The Development of the Classification Approximates the History of Biology Taxonomy– (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 taxonomy Artificial taxonomy

33. Lecture 1 The principles of Classification in Biology

34. Lecture 1 The principles of Classification in Biology

35. Lecture 1 The principles of Classification in Biology

36. Lecture 1 The principles of Classification in Biology

37. Lecture 1 The principles of Classification in Biology Aristotles (384.-322. BC) Scala Naturae, Historia Animalum Gods, Humans, Mammals, Birds, Fishes, Insects, Plants, Minerals.

38. Lecture 1 The principles of Classification in Biology Carl Linneus (1707-1778), Species Plantarum (1753) Systema Naturae (1758) Binary nomenclature

39. Lecture 1 The principles of Classification in Biology Jean Lamarck (1744-1829), Flore Francaise (1778.), Historie Naturelle des Animaux sans Vertebres (1815.-1822.). Inheritance of obtained qualities (1801. –1809.). “Biology” -1802.

40. Lecture 1 The principles of Classification in Biology George Cuvier (1769.-1832.), Animal classification: Vertebrates; Insects, Worms. Paleontology, Theory of Catastrophies.

41. Lecture 1 The principles of Classification in Biology Darwin “On the Origin of Species”: … classification will become genealogy Charles 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.)

42. Lecture 1 The principles of Classification in Biology Ernst 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.”

43. Lecture 1 The principles of Classification in Biology THE MAIN SCHOOLS OF TAXONOMY PHENETIC CLADISTIC MOLECULAR EVOLUTIONARY

44. Lecture 1 The principles of Classification in Biology PHENETIC TAXONOMY Also called numeric or numeral taxonomy.The classification is based on general similarity of morphological or genetic traits.

45. Lecture 1 The principles of Classification in Biology PHENETIC TAXONOMY 1) 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: 23430

46. Lecture 1 The principles of Classification in Biology CLADISTIC TAXONOMY Clade (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) traits

47. Lecture 1 The principles of Classification in Biology MOLECULAR TAXONOMY molecular 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.

48. Lecture 1 The principles of Classification in Biology The 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.

49. Lecture 1 The principles of Classification in Biology EVOLUTIONARY TAXONOMY Darwin “On the Origin of Species”: … classification will become genealogy Uses 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.

50. Lecture 1 The principles of Classification in Biology FIVE KINGDOMS OF LIFE NON-CELLULAR FORMS OF LIFE