Medical Biochemistry, Molecular and Cell Biology I.
2014/15, spring semester
Information on the course and examinations
Name of the Department:
Department of Medical Biochemistry, Faculty of Medicine, Semmelweis University
Name of the course: Medical Biochemistry, Molecular and Cell Biology I.
Neptun code: AOKOBI001_1A
Credits: 7
Director of the course:
Prof. László Tretter M.D., Ph. D., D. Sc.
Description of the curriculum
The principal aim of the course is to provide an insight into the structure and function of
biologically important molecules including amino acids, carbohydrates, lipids and nucleotides
as well as proteins, enzymes and nucleic acids. This module is a prerequisite to the
understanding of the intermediary metabolism of the cell that is introduced by the module of
bioenergetics and mitochondrial ATP production. The cell biology unit describes the
principles of organization of cells as well as the function of subcellular organelles. The
molecular biology module aims at highlighting the storage and expression of genetic
information throughout replication, transcription and translation as well as our current
understanding of the regulation of gene expression, followed by an up-to-date summary of
currently used methods in molecular biotechnology.
Module I. Biologically important molecules and macromolecules
I/1. Amino acids, peptides, proteins
Amino acids. Amino acids as electrolytes. Structure and chirality of amino acids. Reactions of
amino acids. Proteins. The peptide bond. Structure levels in proteins. Primary structure of
proteins. Steric structure of globular proteins. Conformation of proteins. Purification of
proteins. Structural characteristics of fibrous proteins. Collagen. Myoglobin and hemoglobin.
I/2. Enzymology
Enzymes. Enzymes as biocatalysts, enzyme activity. Isoenzymes. Coenzymes. Enzyme
kinetics: the Michaelis-Menten model. Mechanism of action of some important enzymes
(serine proteases). Reversible and irreversible inhibition of enzymes; competitive, noncompetitive and uncompetitive inhibitors. Regulation of enzyme activity. Allosteric enzymes.
I/3. Carbohydrates, lipids, nucleotides
Structure and function of essential building blocks of living cells.
Module II. Bioenergetics and mitochondrial ATP production
Group transfer potential. Bonding types of high group transfer potential. Principle and
examples of coupled reactions in the metabolism. The phosphoryl transfer. Role of high
energy phosphates in the intermediary metabolism. Synthesis of ATP by substrate level
phosphorylation.
Mitochondrial membranes and their permeability. Mitochondrial transporter systems. The
respiratory chain: components, organization, function, inhibitors. Respiratory control, P/O
ratio, uncoupling of oxidative phosphorylation. Mitochondrial ATPase. (FoF1-ATP-ase):
structure, function, inhibitors. Mechanism of oxidative phosphorylation. Chemiosmotic
hypothesis.
Module III. Cell biology
Compartmentation in eukaryotic cells. Membrane structure. Intracellular membranes. Cell
nucleus. Movement of cellular organelles. Cytoskeleton, microfilaments, microtubuli,
actomyosin. Mechanism of vesicular transport. Metabolism and transport, the principle of
metabolom. Metabolic profile of various organelles (endoplasmic retikulum, peroxisomes,
lysosomes, mitochondria).
Module IV. Molecular Biology
IV/1. DNA, RNA and protein synthesis (storage and expression of genetic information)
Nucleic acids – structure and function. Bases, nucleosides, nucleotides, DNA structure, DNA
denaturation, hybridization. DNA replication. Replication in prokaryotes, leading and lagging
strand. Okazaki fragments. DNA-dependent DNA polymerases. DNA ligase. Telomerase.
topoizomerases. Replication in eukaryotes. Structure of eukaryotic chromosomes.
Mitochondrial DNA. Nucleosome structure. DNA repair. Types of DNA damage; mutations,
frameshift, nonsense mutations, mismatch repair. Coordination of repair and replication.
Transcription in procaryotes. Structure of RNA; t-RNA, r-RNA, m-RNA, differences between
the procaryotic and eucaryotic genomes. Transcription complexes, initiation, elongation,
termination in procaryotes. Transcription in eucaryotes, RNA polymerases, promoters,
enhancers, silencers. Processing of mRNA, mechanism of splicing. Alternative splicing,
mRNA editing. The genetic code. Activation of tRNA. Mechanism of translation, initiation,
elongation, termination. Antibiotics. Posttranslational modification of proteins. Protein
folding, sorting, quality control and transport into intracellular compartments. Ubiquitination
and intracellular proteolysis.
IV/2. Regulation of gene expression
Regulation of gene expression in prokaryotes. The operon model. Positive and negative
regulation in the lac operon. Regulation of gene expression in eukaryotes at the transcriptional
level. Role of chromatine structure; covalent and non-covalent chromatin modifying activities
and DNA methylation (epigenetics). Post-transcriptional regulation in eukaryotes. Regulation
of mRNA stability; microRNAs. Translational regulation.
IV/3. The eukaryotic cell cycle and its regulation
Cell cycle in eukaryotes. Cyclins and cyclin dependent protein kinases. Proteases in the cell
cycle. Regulation of G0/G1, G1/S and G2/M transitions. Integration of DNA repair into the
cell cycle.
Module V. Methods in molecular biology and gene technology
Principles of recombinant DNA technology: molecular cloning, restriction endonucleases.
Genomic and cDNA libraries. Blotting techniques (Southern, Northern, Western) and their
utilization. DNA microarrays. PCR and its application in molecular biology. Recombinant
vectors (reporter and expression vectors); synthesis of recombinant proteins. Transgenic,
knock-out and knock-in animals in medical research. Human gene therapy. The Human
Genome Project and its results: organization and polymorphic nature of the human genome;
implications for human traits and diseases. Genotyping methods (PCR-RFLP, PCR-ASA).
Application of bioinformatics in biological and medical research.
Requirements
1. Participation in the laboratory practicals, consultations and seminars is obligatory;
students have to sign the attendance sheets at the end of every lesson. In case of more
than three absences from the practical lessons for any reason, the semester will not be
acknowledged and the student is not allowed to sit for the semifinal exam. Missed
practicals can be completed only in the same week at another group; certificate from
the host teacher should be presented by the student to his/her own teacher. The
schedule of practical lessons, consultations and seminars can be downloaded from the
official homepage of the Institute.
2. Both midterm examinations have to be passed before the commencement of the
examination period (see next paragraph).
Lectures and practical lessons
Two lectures and a laboratory lesson (practical) are held every week; schedules can be found
in separate uploaded files.
Students are expected to keep records and write protocols on the performed experiments
(suggested structure: aim of the experiment, applied methods/devices/reactions, results and
evaluation). Hand-written protocols might be presented either at the end of the lab lesson or at
the beginning of the next practical to the lab teacher. Students might get max. two points for
each acceptable protocol, and points collected this way are added to the total score they
achieve in the corresponding midterm exams. Thus, bonus points collected in weeks 2, 3 and
5 (at most 6) are added to the scores of midterm I and those obtained in weeks 8 – 11 (at most
8) to midterm II, respectively. Importantly, these bonus points not only improve your midterm
grades but might help you pass the midterm, too.
Midterm examinations
Two midterm written examinations will be held during the semester (in weeks 7 and 12 of the
semester, respectively), in frame of the regular laboratory practical lessons. As Tuesday and
Friday in week 12 are holidays (28th April (University Day) and 1st May), groups having
their lab lessons on these days (EM 2-4, 6, 7, 11-14 and ED 1) are going to write Midterm II
in the EOK Szent-Györgyi lecture hall on 27th April (Monday) at 18:05.
Midterm tests consist of open questions that might include structures of bioorganic
compounds as well as calculations with regard to pH of amino acid solutions, enzyme
purification and enzyme kinetics. The material of midterm I covers the subject of lectures and
seminars of the first 6 weeks (corresponding chapters from the topic list: Amino acids,
peptides, proteins and enzymes: 1-18; Carbohydrates: 1-6; Lipids: 1-7; Bioenergetics and
mitochondrial energy production: 1-6). Midterm II is based on the lectures and seminars of
weeks 7-11 (corresponding chapters from the topic list: Nucleotides and nucleic acids: 1-8;
Cell Biology: 1-11; Molecular Biology: 1-33). Midterm tests will be evaluated and graded by
lab teachers (0, 2, 3, 4 or 5 scores).
It is compulsory to pass BOTH midterm exams, that is, to acquire at least 2 scores from each
of them, as a prerequisite to acknowledgement of the semester (obtaining a signature). These
’midterm’ or ’bonus’ points are added to the scores achieved at the semifinal exam (see
below).
Passing both midterms is a prerequisite to acknowledgement of the semester.
Failed midterms might be retaken twice.
The first retake is written; it should be performed in week 8 (retake of midterm I) and week
13 (retake of midterm II), supervised by the student’s own lab teacher.
Students having failed the first retake might sit for the second retake in the last week of the
semester. The second retake is an oral exam conducted by a two-member examination
committee. Students having failed the first retake of both midterms I and II will be examined
in the material of both midterms at the same time.
Semifinal examination
Only those students who successfully completed the semester (requirements: not more than 3
absences from the parcticals and at least 2 scores from each midterm), thus obtained an
official electronic Neptun signature, are entitled to sit for the semifinal exam.
The semifinal is a written exam that consists of two theoretical parts and the lab exam.
First theoretical part: drawing 8 structures selected from the List of obligatory formulas (1
point each), solving a biochemical calculation (amino acids as buffers and enzyme kinetics; 2
points), defining two important terms (1 point each) and providing short answers to open
questions (8 points). The list of obligatory formulas is available in a separate document.
Important terms will be summarized on the last slide of every lecture file.
Second theoretical part: solving 40 multiple choice questions (1 point each).
Practical (lab) exam: an essay question on a laboratory experiment performed during the
semester (evaluation: 0 = unacceptable; 1 point = minor mistakes; 2 points = clear, detailed
and correct). Exact quantities (mass, volume of reagents, incubation times etc.) are not
expected here.
Accordingly, the available total scores in the semifinal test are 20 + 40 + 2 = 62.
The exam is unsuccessful with
- 10 or less points in part 1, OR
- 20 or less points in part 2, OR
- 0 point from the practical exam.
Students having passed both part 1 AND part 2 but failed the practical essay have to retake
only the practical essay when they retake the semifinal exam. Those who want a better grade
are entitled to rewrite the first 2 parts as well, however, with the risk of performing worse.
Students who pass the practical exam but fail either part 1 or part II have to retake both
theoretical blocks but not the practical exam.
In case of successful exams, i. e. when the theoretical part and the practical exam are
successfully completed (at least 11 and 21 points from part I and part II, respectively, and at
least 1 from the lab exam), bonus points from the midterms (at least 4, at most 10) are added
to the total score collected during the exam. Therefore, successful semifinals will be graded as
follows:
33-39 points = grade 2 (pass)
40-49 points = grade 3 (satisfactory)
50-59 points = grade 4 (good)
60-72 points = grade 5 (excellent).
It is possible to write the practical essay in week 14, during the first 15 minutes of the last
laboratory practical of the semester (as a matter of course, the lab experiment of week 14 will
not be asked on this occassion). Students successfully completing this test (getting 1 or 2
points) are exempted from writing the practical exam at the semifinal exam.
It is to note that this is an extra opportunity for passing the practical exam prior to the
beginning of the exam period and in case of failure the semifinal exam should proceed as
outlined above.
Registration and modification of examination dates:
electronically, via the Semmelweis University Neptun System.
Unsuccessful exams can be repeated after three working days at the earliest. All our
examination rules comply with the official examination regulations of the Semmelweis
University.
Textbooks, manuscripts, handouts:
Harper’s Illustrated Biochemistry (30th edition)
Sasvári: Bioorganic compounds (manuscript)
Hrabák: Selected Collection of Chemical Calculations (manuscript)
Medical Chemistry and Biochemistry Laboratory Manual (manuscript)
Powerpoint files of lectures – www.biochemistry.sote.hu, English, For students,
Biochemistry I, authorized pages
(username and password can be obtained from lab teachers)
Students' own lecture notes