BIC-10306 Practical Biological Chemistry

Course

Credits 6.00

Teaching methodContact hours
Lecture11
Tutorial6
Practical90
Independent study0
Course coordinator(s)dr. LMC Nitsch
Lecturer(s)dr. ing. JW Borst
dr. LMC Nitsch
dr. ir. EHM Limpens
dr. LH Beun
WAM van den Berg
dr. HGJM Franssen
dr. VA Willemsen
dr. C Albrecht
R Spruijt
dr. ir. R Heidstra
JA Boeren
Examiner(s)dr. ir. EHM Limpens
dr. LMC Nitsch

Language of instruction:

Dutch

Assumed knowledge on:

CBI-10306 Cell Biology; MIB-10306 Microbiology and Biochemistry

Contents:

Note: This course has a maximum number of participants. The deadline for registration is one week earlier than usual.
See Academic Year.(http://www.wur.nl/en/Education-Programmes/Current-Students/Agenda-Calendar-Academic-Year.htm) -> Registration for Courses.
This introductory practical course provides basic knowledge and skills in molecular biology and biochemistry. Lectures provide the theoretical background of the applied techniques and the experiments to be performed. Subjects are: techniques of gene cloning, structure and function of nucleic acids and proteins, structure and expression of eukaryotic genes, electrophoresis, PCR, hybridization, spectrophotometry and fluorimetry. The practical course consists of a molecular-biological and a biochemical part.
The molecular-biological part is dedicated to: isolation and analysis of DNA, RNA and proteins, both from prokaryotes (E. coli) and eukaryotes (tomato); construction of a physical map of a plasmid by enzyme digestions and electrophoresis; cloning; detection techniques like PCR and the use of computer programs and internet in the analysis of structure and function of DNA (bio-informatics). The gene encoding one of the Rubisco proteins will serve as a model in part of the experiments.
The biochemical part comprises the following subjects: quantitative clinical enzyme assays (uric acid quantitation, enzymatic assay for a heart-attack) and chemo-enzymatic browning of fruit and vegetables, and an introduction to the discovery of cellular protein complexes with proteomics and a computer-assisted design. Additionally a study of the reaction mechanism of an enzyme with kinetics and computer graphics, execution and analysis of spectrometric and fluorimetric enzyme activity assay. At the end of the practical course, students describe their results in short reports. The practical course is concluded with an exam. The final mark is composed of a mark for performance during the practicals (judgment of assistants), a mark for the written reports (judgment of assistants) and the mark for the exam.
The maximal capacity for this course is limited, both in periods 4 and 5. Students for which this course is compulsory or restricted optional will be admitted with priority.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- describe general genome structure and gene organization, transcription and RNA processing in eukaryotes
- understand the principles and explain the use of basic molecular techniques to study genes, such as restriction digestion, agarose gel electrophoresis, cloning, Southern blotting and Western blotting, (RT)-PCR and sequencing
- apply basic techniques in molecular biology, such as DNA, RNA and protein isolation, (RT)-PCR, restriction enzyme digestions, agarose gel electrophoresis, cloning and Western blotting
- understand and apply the principles of absorption- and fluorescence spectroscopy, immunology, electrophoresis, polarography and proteomics
- perform enzymatic assays, interpret data on enzyme catalysis, and relate the results to clinical and nutrition related questions
- use DNA- and protein analysis software (BLAST, 3D-protein structure viewer, proteomics databases)
- calculate and interpret independently the results of their experiments
- write a report about an enzymatic reaction mechanism studied during the laboratorium experiments

Activities:

- attending lectures;
- studying ICT modules;
- performing wet lab and in silico experiments;
- analysing results and writing reports.

Examination:

The Biochemistry and Molecular Biology parts each count for 50% of the final mark. The marks for the Biochemistry and Molecular Biology parts are both calculated from performance and dedication during the practicals and the reports on the experiments (50%) and a test with both multiple choice and open questions (50%). A mark for one of the two tests between 4.5 - 5.4, all other parts having awarded with marks >5.5, results in 5 as a final mark. If the mark for one of the tests is < 4.5, all other parts having awarded with marks > 5.5, the mark for the test will be the final mark. Partial marks remain valid for 6 years.

Literature:

Manual practical course Biological Chemistry, Molecular Biology part (Laboratory of Molecular Biology).
Manual practical course Biological Chemistry, Biochemistry part (Laboratory of Biochemistry).
Griffiths, A.J.F.; [et.al]. (2008). Introduction to genetic analysis. 9th ed. New York, US: Freeman. 839p. ISBN 9780716799023.
Berg, J.M.; Tymoczko, J.L.; Stryer, L.; Gatto, G.J. (2012). Biochemistry. 8th ed. New York [etc.], US: Freeman. 1098p. ISBN 1429276355.
Brightspace: Powerpoint presentations of the lectures.

ProgrammePhaseSpecializationPeriod
Compulsory for: BBIBiologyBScC: Human and Animal Health Biology4WD
BBIBiologyBScA: Cell and Molecular Biology4WD
BBIBiologyBScB: Organismal Adaptation and Development4WD
BBTBiotechnologyBSc5AF
BMLMolecular Life SciencesBSc5AF
BPWPlant SciencesBSc4WD