Synthetic Biology 1

The module Synthetic Biology 1 lays the foundations for understanding current research in synthetic biology,
especially synthetic gene "circuits"

This includes an introduction to the fundamentals of molecular biology as well as quantitative aspects. Content items are:

1. Historical Introduction
2. Biomolecules
3. Bionanoscience
4. Molecular networks
5. Chemical kinetics
6. Dynamical Systems
7. Stochastic Dynamics
8. Synthetic gene circuits
9. Artificial cells

After successful completion of the module the students are able to:

• understand gene expression gene regulatory processes.
• have an overview of current research topics in synthetic biology.
• know how to quantitatively describe gene expression and gene regulation.
• construct basic gene circuits (theoretically).
• undestand nonlinear dynamics and dynamical systems applied to synthetic biological systems.

Basic knowledge in Biophysics and Biochemistry (e.g. PH0020, PH2013 or PH8106)

The lecture introduces basic concepts and discusses them scientifically using a variety of examples from current research. The students should try to understand and penetrate these examples in moredetail at home. Here, the students should actively apply the contents of the lecture,

In addition, the students will use corresponding textbooks (or sections in the textbooks) as well as special literature to deepen the knowledge necessary for the contents of the lecture.

Media/powerpoint presentation and occasional work on the blackboard, transparencies, additional literature, online tools for biophysics/synthetic biology. Literature will be provided via moodle.

• R. Milo & R. Phillips: Biology by the Numbers, Taylor & Francis, (2016)
• R. Phillips, J. Kondev, J. Theriot & H. Garcia: Physical Biology of the Cell, Taylor & Francis, (2012)
• U. Alon: Systems Biology, Taylor & Francis, (2006)
• B. Alberts, A. Johnson, D. Morgan, M. Raff, K. Roberts & P. Walter: Molecular Biology of the Cell, Norton & Company, (2014)
• S.H. Strogatz: Nonlinear Dynamics and Chaos, Westview Press, (2014)

There will be an oral exam of 25 minutes duration. Therein the achievement of the competencies given in section learning outcome is tested exemplarily at least to the given cognition level using comprehension questions and sample calculations.

For example an assignment in the exam might be:

• Describe a possibility to create logic gates.
• How can one create genetic oscillators?
• Describe different possibilities of circuit wiring.
• Describe the Poincare-Bendixson theorem.
• Write down differential equations for simple gene expression.
• Explain the importance of cooperativity in gene regulation.