Download 44401 Molecular biology of the cell

1. COURSE DECRIPTION – GENERAL INFORMATION
1.1. Course teacher
Maja Matulić, Ivica Rubelj
1.2. Name of the course
Molecular biology of the cell
1.3. Associate teachers
1.4. Study programme (undergraduate,
graduate, integrated)
Graduate study of molecular biology
obligatory
1.5. Status of the course
1.6. Year and semester of study
1.7. Credit value (ECTS)
1.8. Type of instruction (number of hours
L+S+E+e-learning)
1.9. Expected enrolment in the course
1.10. Level of use of e-learning (1, 2, 3
level), percentage of instruction in the
course on line (20% maximum)
1st year, W
8
3+1+3
30-40
10 %
2. COURSE DESCRIPTION
2.1. Course objectives
2.2. Enrolment requirements and
required entry competences for the
course
2.3. Learning outcomes at the level of
the study programme to which the
course contributes
2.4. Expected learning outcomes at the
level of the course (4-10 learning
outcomes)
2.5. Course content broken down in
detail by weekly class schedule
(syllabus)
Understanding internal cell organization and its behaviour as a reaction on internal and external influences: making holistic
picture of interconnection of organelle structure, their function and mechanisms of cell regulation. Understanding the processes
in the cell: how are they regulated in dependence on inner cell needs and external signals and which are processes of
differentiation, senescence, proliferation and cell death
cell biology, genetics, biochemistry
connecting previously acquired knowledge from biochemistry, genetics, cell biology with new information in a holistic image of
organization and mechanisms which maintain the cell alive in dependence on external and inner signals
to explain the mechanisms of regulation of intracellular trafficking
to explain the mechanisms of regulation of cellular cytoskeleton
to explain the interrelationship between structure and function of nuclear domains
to explain the pathways of cell cycle regulation and mitosis
to explain the mechanisms of cellular signalling and reaction on extracellular cues
to explain the pathways of cellular processes during differentiation, senescence and cell death
Lectures
1. Introduction: basic structure of eukaryotic cell; endosymbiotic theory
Types of molecular transport in the cell. Endoplasmic reticulum (ER): targeting proteins to and across the ER, protein folding
and quality control in the ER, protein N glycosylation, functions of smooth ER, lipid synthesis, vesicular traffic between ER and
Golgi
2.Structure and function of Golgi apparatus. Protein O-glycosylation, complex glycoprotein synthesis, lysosome structure,
protein targeting to lysosomes, lysosomal storage diseases, mechanisms of retrograde transport, vesicle structure, Rab and
SNARE molecules, endocytic and exocytic pathways, vesicle trafficking in polar cells, transcellular transport.
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3.Posttranslational transport. Targeting of proteins to mitochondria and chloroplasts, structure and formation of peroxisomes,
targeting of peroxisomal proteins, peroxisome functions.
Specific protein synthesis and vesicular traffic in hematopoietic cells and in the defence against microorganisms.
4.Structure and function of the nucleus. Structure of the nuclear envelope and lamina, link between cytosol cytoskeleton and
chromatin through transmembrane proteins of nuclear membrane and nuclear matrix, mechanisms of nuclear envelope
breakdown and reconstitution during mitosis, laminopathies, transport into and out of the nucleus, regulation of transcription
through localization in the nucleus, structure and function of nuclear bodies: nucleolus, Cajal body, PML etc.
5.Cytoskeleton. Basic principles of organization and common feature of three types of cytoskeleton: actin, intermediate
filaments and microtubules. Actin cytoskeleton: basic structure, filament organization, the role of regulatory proteins, molecular
motors, organization and regulation of skeletal muscle contraction and contractile bundles in nonmuscle cells, cell migration,
Rho family proteins, cell polarization and intercellular connections.
6.Microtubules. Basic structure and organization of microtubules, regulatory proteins, molecular motors kinesins and dyneins
and their role in the cell: organelle trafficking and localization, structure of the cilium, centrosome, centrioles, centriole cycle,
functions of sensory cilia, ciliopathies
Intermediate filaments: types and specificities, regulation of lamin polymerization, desmosome structure, neurofilaments.
7.Cell cycle regulation: discovery of the cell cycle mechanism, structure and regulation of maturation promotion factor – cycline
B/cdc2, downstream processes leading to entrance in mitosis, restriction point and regulation of entrance in S phase,
mechanisms of control of DNA replication and proper chromosome segregation in mitosis, role of pRb protein, regulation on
control points in G1 and G2 phase.
Mechanics of mitosis. Processes in prophase, prometaphase, metaphase, anaphase and telophase, mechanisms of spindle
formation and its connection to kinetochores, mechanisms of proper chromosome segregation in metaphase, control of time
and place of cytokinesis, asymmetric division.
8.Extracellular matrix: basic structure of proteoglycans and fibrilar proteins, structure of proteoglycans, collagen, laminin,
fibronectin; structure and function of basal lamina; signalling pathways by which extracellular matrix components regulate the
cellular processes and by which the cell shape the extracellular matrix.
Cell-cell and cell-matrix adhesion. Structure and function of tight junctions, gap junctions, adhesion junctions between cells and
cells and extracellular matrix: adherens junction, focal adhesion, hemidesmosomes, desmosomes, selectins.
9. Signalling in the cell: basic pathways of signalling in the organism, signalling molecules that act locally and at a distance,
discovery of the growth factors, cellular receptors, receptor tyrosine kinases, G protein-coupled receptors, signal transduction
through G proteins, MAP kinase pathway, signalling through protein kinase A and camp, phospholipase C, secondary
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messengers, diacylglycerole, inositol 3 phosphate, survival pathways through phosphatidyl inositol 3 kinase and Akt activation;
Calcium as a messenger, signalling through transcription factor NF kappa B, pathways activated by TGF beta, pathways
connected with cytoskeleton; mechanisms of tumorigenesis connected with signalling pathways
10. Tumour suppressors: basic division according to their function, history of their discovery, pRb, molecules involved in DNA
damage repair as tumour suppressors and their connection with inherited diseases, molecules in developmental pathways as
tumour suppressors: wnt pathway, Hedgehog, neurofibromatosis I and II. Tumour suppressors in the regulation of cell death.
Mechanism of p53 function: mechanisms of its activation, cell and damage specific activation, downstream processes,
signalling shut off.
PoliADPribosylation as a parallel way of DNA damage response.
11. Regulation of gene expression. Mechanisms of regulation of transcription: general and specific transcription factors,
structure of basic types of transcription factors, the role of noncoding RNA and chromatin modifications, histones and DNA as
regulators of transcription, chromatin remodelling by molecular remodelators, principle of combinatorics and regulatory circles in
organism development.
12. Cell differentiation. Characteristics and types of stem cells, regulation of stem cell maintenance, mechanisms of
establishment of induced pluripotent cells and other ways of cellular reprogramming (cell fusion, nuclear transfer), somatic stem
cell niches in the organism: niches of neural, epithelial, hematopoietic and mesenchymal cells. Principles of differentiation:
gradient concentration of morphogenes and contact induction, principles of asymmetric cell division and cellular polarization by
external and intrinsic factors, the role of master transcription factors and principle of combinatorics in development, examples of
cell differentiation in drosophila, in muscle development etc.
13. Aging. Structure and function of telomeres in senescence and carcinogenesis. Theories of aging. Cellular senescence.
Telomere structure. Telomerase. Senescence on the level of the cell and organism. Senescence and carcinogenesis. Aging as
an evolution strategy. Organisms that do not age.
Exercises:
Exercises are organised in the way that allow individual practical work. They are based on the cell culture techniques. Individual
exercises are complete experiments which comprise cell cultivation, their treatment and analysis of collected data. At the end,
students are obliged to write a final report which is analysed together.
1.
2.
3.
4.
5.
6.
Cell cycle analysis by flow cytometry and cell synchronization in the culture
cellular DNA synthesis follow up by incorporation of labelled DNA precursor molecules
apoptosis follow up by staining the cells with fluorescent dyes and their analysis under fluorescent microscope
detection of senescent cells in culture
cell fusion
fluorescent microscopy of cell organelles labelled by molecules fused with green fluorescent protein
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7. follow up of autophagy by acridine orange staining
8. analysis of cell tumorigenicity by growth in “soft agar”
Seminar
Each student will have a seminar made according to scientific article on the topic connected with the lectures which is
broadening certain aspects of given material.
2.6. Type of instruction
2.8. Student responsibilities
2.9. Screening of student’s work (specify
the proportion of ECTS credits for
each activity so that the total number
of CTS credits is equal to the credit
value of the course)):
2.1. Grading and evaluation of student
work over the course of instruction
and at a final exam
x
x
x
lectures
2.7. Comments:
x independent study
seminars and workshops
x multimedia and the internet
exercises
x laboratory
online in entirety
work with the mentor
mixed e-learning
(other)
field work
attendance of lectures, seminars and exercises, written report on excercises, seminar lecture
Research
Practical training
Class attendance
Experimental work
Report
0.4
(Other--describe)
Essay
Seminar essay
Tests
1.8
Oral exam
3.6
(Other—describe)
Written exam
1.8
Project
(Other—describe)
Follow up during seminar lectures and exercises. Possibility of two partial exams.
Title
2.2. Required literature (available at the
library and via other media)
2.12. Optional literature (at the time of
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002): Molecular biology of
the cell, Garland Publishing, New York.
Cooper G. M (2000): The cell: a molecular approach, ASM Press Washington DC,
Sinauer Ass. Sunderland Massachusett
scientific papers in relevant journals
Number of
copies at the
library
3
13
Lodish H, Berk A, Zipursky SL, i sur. (2000): Molecular Cell Biology. 4. ed. New York: W. H. Freeman
4
0.4
Availability via
other media
x
x
x
the submission of the study
programme proposal)
2.13. Methods of monitoring quality that
ensure acquisition of exit
competences
report on exercises, individual seminar lecture, written and oral exam
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