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BIOCHEMISTRY 1 (DEN) 2016/2017)

Lectures

Schedule of Biochemistry, Molecular and Cell Biology 1 lectures

  • Monday 14:40-15:50 Békésy György Lecture Hall EOK Building
  • Tuesday 11:50-13:00 Hevesy György Lecture Hall EOK Building
  • Lecturers: Mária Sasvári MD, PhD, DSc, (MS); Gergely Keszler MD, PhD, (GK); Christos Chinopoulos MD, PhD, (CC);  Miklós Csala MD, PhD,  (MCs); Pál Bauer PhD, (PB);  László Tretter MD, PhD, DSc,  (LT); Beáta Törőcsik MD, PhD, (BT)
Week mm dd Lecture
01 Jan 30 Amino acids. Amino acids as electrolytes. Structure and chirality of amino acids. Reactions of amino acids (MS)
01  Jan 31 Proteins. The peptide bond. Structure levels in proteins. Primary structure of proteins (GK)
02 Feb 06 Steric structure of globular proteins. Conformation of proteins. Purification of
proteins (MS)
02  Feb 07 Structural characteristics of fibrous proteins. Collagen (MS) 
03 Feb 13 Myoglobin and hemoglobin (MS)
03  Feb 14 Enzymes. Enzymes as biocatalysts, enzyme activity. Isoenzymes. Coenzymes (GK)
04 Feb 20 Enzyme kinetics: the Michaelis-Menten model. Mechanism of action of some important enzymes (serine proteases) (MS) 
04  Feb 21 Reversible and irreversible inhibition of enzymes; competitive, non-competitive and uncompetitive inhibitors. Regulation of enzyme activity. Allosteric enzymes (GK) 
05 Feb 27 Compartmentation in eukaryotic cells. Membrane structure. Intracellular  membranes and organelles. Structure and function of the nucleus (MCs)
05 Feb 28 Movement of cellular organelles. Cytoskeleton, microfilaments, microtubuli,actomyosin. Mechanism of vesicular transport (MCs)
06 Mar 06 Metabolism and transport, the principle of metabolom. Metabolic profile of various organelles (endoplasmic reticulum, peroxisomes, lysosomes, mitochondria) (MCs)
06 Mar 07 Principles of bioenergetics: energy transformation, group transfer potential,  coupled reactions, substrate level phosphorylation (CC)
07 Mar 13 Role of mitochondria in biological oxidation. Terminal oxidation (CC)
07 Mar  14 Oxidative phosphorylation (CC) 
08 Mar 20 Nucleic acids – structure and function. Bases, nucleosides, nucleotides, DNA structure, DNA denaturation, hybridization (PB)
08 Mar 21 DNA replication. Replication in prokaryotes, leading and lagging strand,
Okazaki fragments. DNA-dependent DNA polymerases. DNA ligase. Telomerase and topoizomerases. Replication in eukaryotes. Structure of  eukaryotic  chromosomes. Mitochondrial DNA. Nucleosome structure  (PB) 
09 Mar 27 DNA repair. Types of  DNA damage; mutations, frameshift, nonsense
mutations, mismatch repair. Coordination of repair and replication (TB) 
09 Mar 28 Transcription in prokaryotes. Structure of RNA; t-RNA, r-RNA, m-RNA, differences between prokaryotic and eukaryotic genomes.  Transcription complexes, initiation, elongation, termination in prokaryotes (PB)
10 Apr 03 Transcription in eukaryotes, RNA polymerases, promoters, enhancers,
silencers. Processing of mRNA, mechanism of splicing. Alternative splicing. mRNA editing (PB)
10 Apr 04 The genetic code. Activation of tRNA. Mechanism of translation: initiation,
elongation, termination. Antibiotics. Posttranslational modifications of proteins (PB)
      Spring break (Apr 10-14)
11 Apr 17 Eastern Monday
11 Apr 18 Protein folding, sorting, quality control and transport into intracellular compartments. Ubiquitination and intracellular proteolysis (PB)
11 Apr 19 Beznák lecture hall: 17:00-18:10 Regulation of gene expression in prokaryotes. The operon model; positive and negative regulation in the lac operon (LT)
12 Apr 24 Regulation of gene expression at the transcriptional level in eukaryotes. Role of chromatine structure; covalent and non-covalent chromatin modifying activities and DNA methylation (epigenetics) (LT)
12 Apr 25 Post-transcriptional regulation of gene expression in eukaryotes. Regulation of mRNA stability; microRNAs. Translational control (LT)
13 May 01 May Day
13 May 02 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 (BT)
13 May 03 Beznák lecture hall: 17:00-18:10 Principles of recombinant DNA technology: molecular cloning, restriction endonucleases. Genomic and cDNA libraries. Blotting techniques (Southern, Northern, Western) and their utilization. DNA microarrays (BT)
14 May 08 PCR, real-time PCR and their 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 (BT)
14 May 09 The Human Genome Project and its results: organization and polymorphic nature of the human genome; implications for human traits and diseases. Genotyping assays (PCR-RFLP, PCR-ASA). Application of bioinformatics in biological and medical research  (BT)

Laboratory lessons & seminars

Venue: Student laboratories of the Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, EOK Building, 1094 Budapest, Tűzoltó u. 37-47., 1st Floor, Passage „D”

Laboratory lessons and seminars are held Wednesdays, 08:00-10:30 for ED1-2-3-4 groups

01 Feb:01 Carbohydrates (seminar)
02 Feb:08 Precipitation and quantitative determination of proteins. Colour reaction of proteins (lab)
03 Feb:15 Lipids (seminar)
04 Feb:22 SDS-PAGE gel electrophoresis and western blot (lab)
05 Mar:01 Experimental determination of the kinetic parameters of urease (lab)
06 Mar:08 Midterm examination 1
07 Mar:15 National Day
08 Mar:22 Induction of β-galactosidase in bacteria (lab)
09 Mar:29 Restriction digestion of pGL3 basic vector and agarose gel electrophoresis (lab)
10 Apr:05 PCR I
    Springbreak. Easter Monday
11 Apr:19 PCR II
12 Apr:26 Faculty day
13 May:03 Midterm examination 2
14 May:10 Gel filtration (lab)

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.

Both midterm examinations have to be passed before the commencement of the examination period

Groups - Laboratory teachers

Group Day Time Laboratory/seminar teacher
ED1 Wednesday 08:00-10:30 Ambrus, Attila  dr
ED2 Wednesday 08:00-10:30 Bauer, Pál dr
ED3 Wednesday 08:00-10:30 Dóczi, Judit dr
ED4 Wednesday 08:00-10:30 Végh, Miklós dr

Text books

  • 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

Midterm exams

Two midterm written examinations will be held during the semester (in weeks 6 and 13 of the semester, respectively), during laboratory practical lessons.

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 4 weeks (corresponding chapters from the topic list: Amino acids, peptides, proteins and enzymes: 1-18; Carbohydrates: 1-6; Lipids 1-3).

Midterm II is based on the lectures and seminars of weeks 5-12 (corresponding chapters from the topic list: Cell Biology: 1-11; Bioenergetics and mitochondrial energy production: 1-4; Nucleotides and nucleic acids: 1-8; Molecular Biology: 1-35). 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).

The midterm test consists of four theoretical questions (10 points each) and two problems (calculations; 10 points each). Midterm tests will be evaluated by lab teachers and marked as 0, 2, 3, 4 or 5.

Grading of midterms (total scores include points obtained from lab reports (at most 6)):

  • 0 – 30 points: 0
  • 31 – 38 points: 2
  • 39 – 46 points: 3
  • 47 – 53 points: 4
  • 54 or more points: 5

Relevant chapters from Harper’s Biochemistry, 30th edition: 3, 5, 6, 7, 8, 9; 11, 12; 15

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 7 (retake of midterm I) and week 13 or 14 (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.

2nd oral(retake) midterm exam

This exam is held on the 12th of May, 2017 at 09:40. We ask our students to contact Mrs. Veronika Pichler in room 1.508 at 09:30.

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.

Semi-final examination

Topic list

DOWNLOADS

Biochemistry, Molecular and Cell Biology 1

Subject matter Biochemistry, Molecular and Cell Biology 1

  • Name of the course: Biochemistry, Molecular and Cell Biology 1
  • Neptun code: FOKOOBI159_1A Credits: 7  Lectures:Practicals:3
  • Director of the course: Prof. Tretter, László MD, PhD, DSc
  • Semi-final examination

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, vitamins, coenzymes (descriptive biochemistry), as well as proteins, enzymes and nucleic acids. This module is a prerequisite to the understanding of the intermediary metabolism of the cell. 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.