BASIC CELL BIOLOGY I CHEMISTRY of LIFE Indriis

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. • 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, 1996 Unit 1 (pp. 25 -103) Chapter 23 (pp. 469 479)

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)

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 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

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

Lecture 1 NATURAL SCIENCES PHYSICS ASTRONOMY CHEMISTRY GEOGRAPHY GEOLOGY BIOLOGY: 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 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, M 38, Dec. 1999) TELEOLOGY - DOES THE NATURE HAVE PURPOSE ?

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 HEREDITY AND MUTATION IMMUNOLOGY GENETICS FUNCTIONS OF PHYSIOLOGY ORGANS AND SYSTEMS DEVELOPMENT EMBRIOLOGY, DEVELOPMENTAL BIOLOGY METABOLISM BIOCHEMISTRY, BIOPHYSICS

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

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

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

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

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

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

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

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

Branches of Biology Lecture 1 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

Principles of Studies in Biology Lecture 1 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 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

Principles of Studies in Biology Lecture 1 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

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

Principles of Studies in Biology Lecture 1 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)

Principles of Studies in Biology Lecture 1 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 )

The Principles of Studies in Biology Lecture 1 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

The Principles of Studies in Biology Lecture 1 Methodological Approaches Holism 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.

The Principles of Studies in Biology Lecture 1 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.

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

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 MICOLOGY CHEMISTRY ANATOMY BOTANY PHYSICS MORPHOLOGY ZOOLOGY TAKSONOMY Objects Structure

The Principles of Studies in Biology Lecture 1

The principles of Classification in Biology Lecture 1 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

The principles of Classification in Biology Lecture 1

The principles of Classification in Biology Lecture 1

The principles of Classification in Biology Lecture 1

The principles of Classification in Biology Lecture 1

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

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

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

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

The principles of Classification in Biology Lecture 1 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. )

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. ”

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

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

The principles of Classification in Biology Lecture 1 PHENETIC TAXONOMY 1) Voges-Proskauer (VP); 2) Nitrate(N); 3) Phe-deaminase (PD); 4) H 2 S; 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

The principles of Classification in Biology Lecture 1 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

The principles of Classification in Biology Lecture 1 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.

The principles of Classification in Biology Lecture 1 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.

The principles of Classification in Biology Lecture 1 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.

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

The principles of Classification in Biology THREE DOMAINS OF LIFE Lecture 1