Cipher: 2503
Nomenclature: Kinetics of enzymatic reactions
Study programme: Molecular biosciences
Module: Plant biology
Case holder:

Izv.prof.dr.sc. Valentina Pavić
Institution of the case holder:

J.J. Strossmayer University of Osijek, Department of Biology
Contributors - Contractors:
Subject status: Electoral College
The year in which the case is submitted: Year I
The semester in which the case is submitted: Semester II
Subject objective:

To know the kinetics of enzymatic reactions, possibilities and techniques of monitoring the speed of enzymatic reactions, kinetic models, kinetic constants and their determination and inhibitors and types of inhibition of enzymatic reactions, as well as the application of these findings when clarifying metabolic and molecular biological processes.
Case contents:

• Basic principles of enzymatic catalysis
• Thermodynamic changes in enzymatic systems
• Units expressing enzyme activity
• Changes in participants' concentration during enzymatic reaction
• Michaelis-Menten model, kinetic constants KM and Vmax and their meaning
• Kinetics of allosteric enzymes
• Ways to measure the speed of enzymatic reactions
• Inhibition of enzymatic reactions, inhibition types, changes in kinetic constants of inhibited enzymatic reactions
• Kinetics of enzymes in physiological systems
• Regulation of metabolic processes by kinetic traits of some enzymes
Learning outcomes: competences, knowledge, skills that the subject develops:

1. Adjust optimal reaction conditions in relation to your own analyzed biological material.
2. Carry out the measurement of the speed of the enzymatic reaction in the biological material and express the obtained results in an appropriate and normal manner.
3. Determine the basic kinetic constants and discuss the results obtained, and monitor the effect of inhibitors on enzymes in selected biological systems.
4. Apply acquired knowledge and literature data when clarifying metabolic and molecular biological processes.
ECTS Credits 6
Lectures 20
Seminars (IS) 5
Exercises (E) 5
Altogether 30
The way of teaching and acquiring knowledge:

Regular attendance (maximum absence of 2h lectures); exercises, i.e. laboratory work must be done in its entirety.
Ways of teaching and acquiring knowledge: (notes)
Monitoring and evaluating students (mark in fat printing only relevant categories) Attendance, Teaching activities
Rating method: Written exam, Oral exam, Publication analysis, Continuous verification of knowledge in the course of teaching
Mandatory literature:

1. Nelson D. L., Cox M.M. (2013) Lehninger principles of biochemistry, W. H. Freeman & Co., 6th ed. York
2. Cornish-Bowden A. (2004) Fundamentals of Enzyme Kinetics, revised Edition, Portland Press, London
Supplementary (recommended) literature:

1. Adamczyk, Malgorzata, Karen van Eunen, Barbara M. Bakker, and Hans V. Westerhoff. 2011. "Enzyme Kinetics for Systems Biology When, Why and How." Methods in Enzymology 500: 233–57. doi:10.1016/B978-0-12-385118-5.00013-X.
2. Berg, Jeremy M., John L. Tymoczko, Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, and Lubert Stryer. 2002 Biochemistry. 5th ed. W H Freeman.
3. Boo, H.-. 2006. "A Literature Review of Enzyme Kinetic Parameters for CYP3A4-Mediated Metabolic Reactions of 113 Drugs in Human Liver Microsomes: Structure- Kinetics Relationship Assessment." Current Drug Metabolism 7 (3): 231–49. doi:10.2174/138920006776359329.
4. Chow, Melissa L., Laura Troussicot, Marie Martin, Bastien Doumèche, Florence Guillière, and Jean-Marc Lancelin. 2016. "Predicting and Understanding the Enzymatic Inhibition of Human Peroxiredoxin 5 by 4-Substituted Pyrocatechols Combining Funnel-Metadynamics, Solution NMR and Steady-State Kinetics." Biochemistry, May. doi:10.1021/acs.biochem.6b00367.
5. Deschamps, Joshua D., Abiola F. Ogunsola, J. Brian Jameson, Adam Yasgar, Becca A. Flitter, Cody J. Freedman, Jeffrey A. Melvin, et al. 2016. "Biochemical/Cellular Characterization and Inhibitor Discovery of Pseudomonas Aeruginosa 15-Lipoxygenase." Biochemistry, May. doi:10.1021/acs.biochem.6b00338.
6. Durruty, Ignacio, Luis A. N. Aguirrezábal, and María M. Echarte. 2016. "Kinetic Modeling of Sunflower Grain Filling and Fatty Acid Biosynthesis." Frontiers in Plant Science 7: 586. doi:10.3389/fpls.2016.00586.
7. Filatova, Lyubov Y., David M. Donovan, Nadiya T. Ishnazarova, Juli A. Foster-Frey, Stephen C. Becker, Vladimir G. Pugachev, Nadezda G. Balabushevich, Natalia F. Dmitrieva, and Natalia L. Klyachko. 2016. "A Chimeric LysK-Lysostaphin Fusion Enzyme Lysing Staphylococcus Aureus Cells: A Study of Both Kinetics of Inactivation and Specifics of Interaction with Anionic Polymers." Applied Biochemistry and Biotechnology, May. doi:10.1007/s12010-016-2115-7.
8. Ghneim, H.K. 2016. "The Kinetics of the Effect of Manganese Supplementation on SOD2 Activity in Senescent Human Fibroblasts." European Review for Medical and Pharmacological Sciences 20 (9): 1866–80.
9. Li, Pu, and Quoc Dong Vu. 2013. "Identification of Parameter Correlations for Parameter Estimation in Dynamic Biological Models." BMC Systems Biology 7: 91. doi:10.1186/1752-0509-7-91.
10. Li, Pu, and Quoc Dong Vu. 2015. "A Simple Method for Identifying Parameter Correlations in Partially Observed Linear Dynamic Models." BMC Systems Biology 9: 92nd doi:10.1186/s12918-015-0234-3.
11. Marangoni, Alejandro G. 2002. Enzyme Kinetics. Hoboken, NJ, USA: John Wiley & Sons, Inc. http://doi.wiley.com/10.1002/0471267295.
12. Rubin, Katy J., and Peter Sollich. 2016. "Michaelis-Menten Dynamics in Protein Subnetworks." The Journal of Chemical Physics 144 (17): 174114. doi:10.1063/1.4947478.
13. Sawlekar, Rucha, Francesco Montefusco, Vishwesh V. Kulkarni, and Declan G. Bates. 2016. "Implementing Nonlinear Feedback Controllers Using DNA Strand Displacement Reactions." IEEE Transactions on Nanobioscience, April. doi:10.1109/TNB.2016.2560764.
14. Tummler, Katja, Timo Lubitz, Max Schelker, and Edda Klipp. 2014. "New Types of Experimental Data Shape the Use of Enzyme Kinetics for Dynamic Network Modeling." The FEBS Journal 281 (2): 549–71. doi:10.1111/febs.12525.
How to monitor the quality and performance performance (evaluation):

• Discussions with students and colleagues.
• Monitoring each student's progress.
• The success of the course will be evaluated annually by the joint expert committee of the Rudjer Boskovic Institute, the University of Dubrovnik and the University of Josip Juraj Strossmayer in Osijek.