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

BASIC CELL BIOLOGY

I CHEMISTRY of LIFEIndriķis Muižnieks

II STRUCTURE OF THE CELLTūrs Selga

I CHEMISTRY OF LIFE

• Basic Principles of the Metabolism.

• 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.

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 andL.G. Mitchell BIOLOGY, Benjamin Cummings Publ., 5-th edition, 1999IntroductionUnit 1 (pp. 20-100)

READING:

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

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 characterizedby 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, M38, Dec. 1999)

TELEOLOGY - DOES THE NATURE HAVE PURPOSE ?

Lecture 1

Structural and functional diversity of biological systems.

Lecture 1

FUNCTIONS

METABOLISM

DEVELOPMENT

FUNCTIONS OF ORGANS AND

SYSTEMS

HEREDITY AND MUTATION

INTERACTIONS WITH COUNTERPARTS

INTERACTIONS WITH THE ENVIRONMENT

ORIGIN OF SPECIES

BIOCHEMISTRY, BIOPHYSICS

EMBRIOLOGY, DEVELOPMENTAL BIOLOGY

PHYSIOLOGY

GENETICS

POPULATION BIOLOGY

ECOLOGY

EVOLUTION

IMMUNOLOGYMANTENANCE OF IDENTITY

STRUCTURE

MOLECULES

MACROMOLECULES

CELLS

TISSUES

ORGANISMS

SPECIES

DIVERSITY OF LIFE


MOLECULAR BIOLOGY

CYTOLOGY, CELL BIOLOGY

HISTOLOGY

MORPHOLOGY

SYSTEMATICS

TAXONOMY

ANATOMYORGANS, SYSTEMS


Lecture 1

OBJECTS

NON-CELLULAR FORMS OF LIFE

BACTERIA

FUNGI

PLANTS

ANIMALS

VIROLOGY

BACTERIOLOGY

MYCOLOGY

BOTANY

ZOOLOGY

PROTISTOLOGYUNICELLULAR ORGANISMS


Lecture 1

OBJECTS

SPECIALISATIONS OF BIOLOGY

The study of the specific structures and functions of defined objects.

Plant AnatomyBacterial geneticsAnimal PhysiologyMolecular biology of the Viruses

Branches of BiologyLecture 1


DEVELOPME NTAL BILOGY

PHYSI OLOGYGENE TICS

POPULATION BIOLOGY ECO LOGYEVOL UTION

MOLECULAR BIOLOGY

CITOLOGY

HISTOLOGY

ANATOMY

MORPHOLOGYTAKSONOMY

VIROLOGY

BACTERIOLOGYPROTISTOLOGYMICOLOGY

BOTANYZOOLOGY

Functions

Structure

Objects

IMMUN OLOGY

FURTHER SUBDIVISION OF THE BRANCHES

BOTANY Trees Dendrology

AlgaePhycology

Mosses Briology

Lichens Lichenology


ZOOLOGY Mammals Mammology

Birds Ornithology

Reptiles and Herpetology

amphibians

Fishes Ichtiology

Insects Entomology

Molluscs, snailsMalacology


FURTHER SUBDIVISION OF THE BRANCHES

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


METHODS OF INVESTIGATION

Visualisation of the objects and structures

Microscope

Genetical engineering

Biometry

Construction of self-replicating nucleic acids in vitro

Data processing and assessment






MOLECULAR BIOLOGY

CITOLOGY

HISTOLOGY

ANATOMY

MORPHOLOGYTAXONOMY

VIROLOGY


BOTANYZOOLOGY

Functions

Structure

Objects

IMMUN OLOGY


The use of the knowledge from other branches of science for the development of biological research.

Reflecting sub-branches

Biochemistry, Biophysics, Paleobiology, Zoogeography.

Large projections

Versatile application of the Biological knowledge in the other field of science.Biotechnology, Environment Sciences, Biomedicine


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.

Principles of Studies in Biology

The Scientific MethodHypothesisAssumption, 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 1

Scientific MethodTheory

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 itsForce of deduction - capability to create testable hypothesisNothing is as practical as a good theory

Lecture 1Principles of Studies in Biology

THEORY

HYPOTHESISCONCLUSION (observation,

fact) VALIDATION

INDUCTION DEDUCTION

EXPERIENCE

EXPLANATION

Lecture 1

Scientific Method


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)

Lecture 1Principles of Studies in Biology

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 1

Methods of Assessment


The Principles of Studies in Biology

Methodological Approaches

Reductionisma 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

Lecture 1

The Principles of Studies in Biology

Methodological Approaches

Holism 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 1

Didactic 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.

The Principles of Studies in BiologyLecture 1

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.


CHEMISTRYPHYSICS





MOLECULAR BIOLOGY

CITOLOGY

HISTOLOGY

ANATOMY

MORPHOLOGYTAKSONOMY

VIROLOGY


BOTANYZOOLOGY

Functions

Structure

Objects

IMMUN OLOGY


The principles of Classification in Biology

The 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 taxonomy

Artificial taxonomy

Lecture 1

The principles of Classification in BiologyLecture 1

Aristotles

(384.-322. BC) Scala Naturae,

Historia Animalum

Gods, Humans, Mammals, Birds, Fishes, Insects,

Plants, Minerals.


Carl Linneus

(1707-1778), Species

Plantarum (1753)

Systema Naturae (1758)

Binary nomenclature


Jean Lamarck

(1744-1829), Flore Francaise

(1778.),

Historie Naturelle des Animaux sans

Vertebres (1815.-1822.).

Inheritance of obtained qualities

(1801. –1809.).

“Biology” -1802.


George Cuvier

(1769.-1832.), Animal

classification: Vertebrates;

Insects, Worms.

Paleontology, Theory of

Catastrophies.


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.)


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 MAIN SCHOOLS OF TAXONOMY

PHENETIC

EVOLUTIONARY

CLADISTIC

MOLECULAR


PHENETIC TAXONOMYAlso called numeric or numeral taxonomy.

The classification is based on general similarity of morphological or genetic traits.


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

PHENETIC TAXONOMYThe principles of Classification in Biology

Lecture 1

CLADISTIC TAXONOMYThe principles of Classification in Biology Lecture 1

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

MOLECULAR 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.


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.


EVOLUTIONARY TAXONOMY

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.


Darwin “On the Origin of Species”: … classification will become genealogy

FIVE KINGDOMS OF LIFE

NON-CELLULAR FORMS OF LIFE


THREE DOMAINS OF LIFE


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

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