P1252428425Evhci

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BASIC CELL BIOLOGY
I CHEMISTRY of LIFE
Indrikis Muižnieks
II STRUCTURE OF THE CELL
Turs Selga
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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.

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

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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

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Lecture 1
SCIENCES
HUMANITIES SOCIAL MEDICAL AGRICULTURAL ENGINEERING
EDUCATION NATURAL and MATHEMATICS
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Lecture 1
NATURAL SCIENCES
PHYSICS ASTRONOMY CHEMISTRY GEOGRAPHY GEOLOGY BIOL
OGY
study of living things and their vital processes.
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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

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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 ?
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Lecture 1
Structural and functional diversity of biological
systems.
FUNCTIONS
ORIGIN OF SPECIES
EVOLUTION
INTERACTIONS WITH THE ENVIRONMENT
ECOLOGY
INTERACTIONS WITH COUNTERPARTS
POPULATION BIOLOGY
IMMUNOLOGY
MANTENANCE OF IDENTITY
HEREDITY AND MUTATION
GENETICS
FUNCTIONS OF ORGANS AND SYSTEMS
PHYSIOLOGY
DEVELOPMENT
EMBRIOLOGY, DEVELOPMENTAL BIOLOGY
METABOLISM
BIOCHEMISTRY, BIOPHYSICS
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Lecture 1
Structural and functional diversity of biological
systems.
STRUCTURE
DIVERSITY OF LIFE
TAXONOMY
SPECIES
SYSTEMATICS
ORGANISMS
MORPHOLOGY
ANATOMY
ORGANS, SYSTEMS
TISSUES
HISTOLOGY
CELLS
CYTOLOGY, CELL BIOLOGY
MACROMOLECULES
MOLECULAR BIOLOGY
MOLECULES
BIOCHEMISTRY, BIOPHYSICS
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Lecture 1
Structural and functional diversity of biological
systems.
OBJECTS
ANIMALS
ZOOLOGY
PLANTS
BOTANY
FUNGI
MYCOLOGY
PROTISTOLOGY
UNICELLULAR ORGANISMS
BACTERIA
BACTERIOLOGY
NON-CELLULAR FORMS OF LIFE
VIROLOGY
OBJECTS
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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
Molecular biology of the Viruses
GENE TICS
PHYSI OLOGY
DEVELOPME NTAL BILOGY
BIOCHEMISTRY, BIOPHYSICS
MOLECULAR BIOLOGY
VIROLOGY
CITOLOGY
BACTERIOLOGY
PROTISTOLOGY
HISTOLOGY
MICOLOGY
ANATOMY
BOTANY
MORPHOLOGY
ZOOLOGY
TAKSONOMY
Objects
Structure
SPECIALISATIONS OF BIOLOGY
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Lecture 1
Branches of Biology
FURTHER SUBDIVISION OF THE BRANCHES
BOTANY
Trees Dendrology Algae Phycology Mosses Briolog
y Lichens Lichenology
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Lecture 1
Branches of Biology
FURTHER SUBDIVISION OF THE BRANCHES
ZOOLOGY
Mammals Mammology Birds Ornithology Reptiles
and Herpetology amphibians Fishes Ichtiology In
sects Entomology Molluscs, snails Malacology
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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
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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
MOLECULAR BIOLOGY
VIROLOGY
CITOLOGY
BACTERIOLOGY
PROTISTOLOGY
HISTOLOGY
MICOLOGY
ANATOMY
METHODS OF INVESTIGATION
BOTANY
MORPHOLOGY
ZOOLOGY
TAXONOMY
Structure
Objects
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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.
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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
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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

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

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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 )

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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
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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.
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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.
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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.
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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
MOLECULAR BIOLOGY
VIROLOGY
CITOLOGY
BACTERIOLOGY
PROTISTOLOGY
HISTOLOGY
CHEMISTRY PHYSICS
MICOLOGY
ANATOMY
BOTANY
MORPHOLOGY
ZOOLOGY
TAKSONOMY
Structure
Objects
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Lecture 1
The Principles of Studies in Biology
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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
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Lecture 1
The principles of Classification in Biology
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Lecture 1
The principles of Classification in Biology
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Lecture 1
The principles of Classification in Biology
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Lecture 1
The principles of Classification in Biology
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Lecture 1
The principles of Classification in Biology
Aristotles (384.-322. BC) Scala Naturae,
Historia Animalum Gods, Humans, Mammals, Birds,
Fishes, Insects, Plants, Minerals.
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Lecture 1
The principles of Classification in Biology
Carl Linneus (1707-1778), Species Plantarum
(1753) Systema Naturae (1758) Binary nomenclature
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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.
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Lecture 1
The principles of Classification in Biology
George Cuvier (1769.-1832.), Animal
classification Vertebrates Insects, Worms.
Paleontology, Theory of Catastrophies.
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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.)
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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.
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Lecture 1
The principles of Classification in Biology
THE MAIN SCHOOLS OF TAXONOMY
PHENETIC
CLADISTIC
MOLECULAR
EVOLUTIONARY
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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.
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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
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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
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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.
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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.
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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.
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Lecture 1
The principles of Classification in Biology
FIVE KINGDOMS OF LIFE
NON-CELLULAR FORMS OF LIFE
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Lecture 1
The principles of Classification in Biology
THREE DOMAINS OF LIFE