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, M38, 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
MOLECULES
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 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
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
HYPOTHESIS
(observation,
fact)
VALIDATION
EXPERIENCE
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
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.
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 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.
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) 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
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