
Synthetic Biology
Code: 107533Credits: 6
| Degree programme | Type | Course |
|---|---|---|
| Biotechnology | OP | 4 |
Contact lecturer
- Name :
- Marc Torrent Burgas
- Email :
- marc.torrent@uab.cat
Teaching staff
- Susanna Navarro Cantero
Group languages
You can consult this information at the end of the document.
Prerequisites
There are no prerequisites for this course, but it is recommended to have taken courses in molecular biology as well as chemistry, and protein engineering.
Objectives
This course aims to introduce students to Synthetic Biology as an interdisciplinary field combining molecular biology, genetic engineering, chemistry and computational biology. Through lectures, practical sessions, and a research project, students will acquire the conceptual and experimental tools required to:
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Understand the foundations of synthetic biology and how it differs from traditional genetic engineering.
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Design and analyze genetic circuits, biological computers, and molecular regulatory systems.
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Learn strategies for the de novo design of genomes, proteins, and metabolic pathways using computational models and artificial intelligence.
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Apply this knowledge to the creation of organisms with novel functions, such as live biotherapeutics, biosensors, and engineered microbes.
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Reflect on the ethical, legal, and societal implications of synthetic biology, including biohacking, human enhancement, and genetic code modification.
Learning outcomes
- CM25 (Work collaboratively in teams to solve problems in the field of systems biology.) Work collaboratively in teams to solve problems in the field of systems biology.
- KM27 (Determine the environmental impact of the use of synthetic biology in biotechnological production.) Determine the environmental impact of the use of synthetic biology in biotechnological production.
- SM23 (Use the fundamentals of mathematics, physics and chemistry necessary for the study of regulatory mechanisms at the molecular level in living beings.) Use the fundamentals of mathematics, physics and chemistry necessary for the study of regulatory mechanisms at the molecular level in living beings.
- SM24 (Quantitatively model a biological process or system.) Quantitatively model a biological process or system.
Contents
I. Introduction to Synthetic Biology
Module 1: Fundamentals of Synthetic Biology
Definition and scope.
History and evolution of synthetic biology.
Differences from traditional genetic engineering.
Impact on biotechnology and biomedicine.
Goals and challenges of synthetic biology.
II. Biological Design
Module 2: Biological Circuits and Molecular Computers
Fundamentals of genetic circuits.
Gene regulation: promoters, repressors, and other elements.
Strategies for modularity and circuit reconfiguration.
Genetic switches, oscillators, and bistable behavior.
Transcriptional and post-transcriptional regulation.
Use of evolutionary algorithms to optimize genetic circuit designs.
Building biological computers.
Implementation of logic gates at the cellular level.
Biological sensors and detection systems.
Biocomputation and cellular memory.
Simulations and experimental prototypes.
Module 3: Design of Synthetic Organisms
Synthesis of artificial genomes.
Construction of minimal genomes: the case of Mycoplasma laboratorium.
Large-scale DNA assembly and synthesis protocols.
Engineering complete genomes using artificial intelligence.
Optimization of cellular chassis for industrial applications.
Generation of new enzymes and metabolic pathways.
AI models for macromolecule design.
Artificial biological catalysis.
Creation of new chemical and pharmaceutical products in silico.
Biotechnological applications of de novo design.
Design of synthetic photosynthetic organisms.
Production of biopharmaceuticals and biocompatible materials.
Environmental biosensors.
Synthetic organisms in bioenergy.
III. Applications of Synthetic Biology
Module 4: Living Pills and Therapeutic Microorganisms
Engineering therapeutic microbiomes.
Microbes as drug factories within the body.
Engineered bacteria for disease detection and treatment.
Modulation of immune responses through modified microorganisms.
Strategies to avoid adverse immune reactions.
Legislation and biosafety regulations.
Risk-benefit assessments in humans.
Module 5: Modification and Expansion of the Genetic Code
Incorporating new amino acids into the genetic code.
Molecular foundations of genetic code engineering.
Genetic code expansion. Orthogonality. Engineered tRNA transferases and synthetases.
Production of fluorescent proteins, synthetic catalysts, and novel materials.
Evolutionary consequences and safety of expanded genetic codes.
Long-term effects in cells and organisms.
Biocontainment and strategies to prevent horizontal gene transfer.
Module 6: Biohacking, Human Enhancement, and Ethics
Biohacking and experimentation in synthetic biology.
Notable biohacking cases and DIYbio communities.
Legal and regulatory limitations.
Human enhancement and brain-machine interfaces.
Genetics of human enhancement: possibilities and technical limitations.
Enhanced abilities: physical (myostatin and FOXP2), cognitive (regulation of SCN9A and NR2B), and sensory (modification of opsin 1, PDE6H or TMC1).
Engineering symbiotic bacteria to improve detoxification or nutrient absorption.
Regulation of aging, organic rejuvenation, and consciousness transfer.
Brain-machine interfaces and digital telepathy: Applications of Neuralink, BrainGate, Kernel, or NextMind.
Learning activities and methodology
| Title | Hours | ECTS | Learning outcomes |
|---|---|---|---|
| Tutorials in classroom | 4 | 0.16 | SM23, SM24 |
| Problems/specific subjects | 10 | 0.4 | CM25, KM27, SM23 |
| Individual study | 67 | 2.68 | SM23 |
| Research project | 12 | 0.48 | CM25, KM27, SM23, SM24 |
| Individual study of specific subjects | 15 | 0.6 | SM23 |
| Lectures | 35 | 1.4 | KM27, SM23, SM24 |
Lectures
Lectures are a fundamental component of the course and are designed to provide a solid and well-structured foundation of the most relevant content. In addition to explaining key concepts, the instructor will encourage active participation through open questions, brief debates, and contextualized examples that help connect theoretical content to real-world cases and practical applications. These sessions also offer the opportunity to interact directly with the instructor and peers, clarify doubts in real time, and consolidate learning in a more dynamic and participatory way. All materials will be available at the Moodle virtual area.
Problem-solving sessions
These sessions aim to reinforce theoretical knowledge through the analysis and resolution of exercises based on the course content. Two complementary formats will be used:
1. Structured problems. At the end of each thematic unit, students will work on closed or semi-open problems designed to practice and internalize the fundamental concepts—such as the design of genetic circuits. These exercises help identify specific challenges and strengthen understanding of basic tools.
2. Contextualized and open-ended problems. As the course progresses, more complex and realistic scenarios will be introduced. These will require integrating knowledge, making justified decisions, and exploring alternative solutions. These problems will be solved in small groups to promote active participation,collaborative reasoning, and critical discussion. Evaluation will consider both the resolution process and the ability to justify and communicate decisions.
Group tutorials
Tutorial sessions are designed as spaces for academic guidance and support. The main objective is to help students plan and approach the autonomous learning components of the course effectively. The instructor will provide strategies to organize study time, identify key concepts, and make optimal use of the available learning materials. These sessions will also offer an opportunity to address general questions, share common difficulties, and reflect on the learning process itself.
Assessment
Continuous assessment activities
| Title | Weight | Hours | ECTS | Learning outcomes |
|---|---|---|---|---|
| Laboratory practical sessions | 25% | 0.5 | 0.02 | CM25, SM23, SM24 |
| Oral presentation | 10% | 0.5 | 0.02 | CM25, KM27, SM23, SM24 |
| Research project | 40% | 3 | 0.12 | CM25, SM23, SM24 |
| Written exam | 25% | 3 | 0.12 | CM25, KM27, SM23, SM24 |
Continuous assessment
The assessment of this course is based on four components combining individual and group work, practical application, and theoretical reasoning. The goal is to evaluate both conceptual understanding and the ability to integrate and apply knowledge in a critical and creative way.
1. Research project (40%)
Each student will develop a research project on a topic related to synthetic biology, either proposed by the student or suggested by the instructor. The project must integrate the knowledge acquired during the course, with particular emphasis on Block II (biological design). The objective is not to produce a conventional literature review, but to apply the acquired knowledge to address a relevant scientific question or respond to a current technological need.
Projects will be presented and assessed through a peer review system involving the entire class. This dynamic encourages critical thinking and collective engagement. The course instructor will also evaluate the research project and reserves the right to modify the grades if any bias is detected during the review. At the end of the course, all projects will be compiled into a collaborative digital journal.
Submitted assignments are not eligible for resubmission or recovery.
2. Oral presentation of the research project (10%)
Each group will give an oral presentation, lasting approximately 10 minutes, of the research project carried out during one of the class sessions. Evaluation will consider argumentation skills, clarity of presentation, and teamwork.
3. Laboratory practicals (25%)
Assistance to the laboratory practials is required to pass the course. Lab sessions provide hands-on experience with experimental tools relevant to synthetic biology. Assessment will be based on an individual report analyzing the results obtained, the methodology used, and the interpretation of the observed phenomena. Critical analysis, clarity of writing, and scientific rigor will be valued.
4. Written exam (25%)
The written exam will assess the student’s understanding of the fundamental concepts of the course, as well as reasoning ability and content integration. It will include both conceptual and applied questions. Any material covered in lectures, problem sessions, or independent study may be included. A minimun of 4 points in the written exam is required to pass de course.
The course will be considered passed when the total weighted score is equal to or greater than 5 out of 10, if all conditions are met for all evaluation parts.
To be eligible for evaluation, students must have been assessed in activities representing at least two-thirds (67%) of the course’s total assessment weight. Students will receive a “Not Assessable” mark if their assessed activities account for less than 67% of the final grade.
NOTES:
Students may use Artificial Intelligence (AI) tools as part of their coursework, provided the final result clearly grounded in the student's own analysis and critical thinking. Students must clearly state which parts were generated using AI, list the tools used, and include a critical assessment on how these tools shaped the process and the final outcome. Failing to disclose AI use is considered academic misconduct and may lower the grade for the activity or, in serious cases, lead to disciplinary action.
Academic misconduct in any assessment activity (academic fraud, plagiarism, or improper use of AI, unless such use is expressly authorized in the course syllabus) that significantly affects the score will earn a grade of 0 on that activity. If the syllabus requires a minimum score on that activity as a requirement for passing the course, or if multiple such violations occur within the same course, the student's final grade for the course will be 0. In addition, the student may also face disciplinary action.
This course does not offer a single final assessment option.
Bibliography
Lehninger: Principles of Biochemistry. D.L. Nelson & M.M. Cox (2021) 8th edition, W. H. Freeman.
Biobuilder: Synthetic Biology in the Lab. Natalie Kuldell, Rachel, Bernstein, Karen Ingram & Kathryn Hart (2015) 1st edition, O'Reilly Media
Synthetic Biology: From iGEM to the Artificial Cell. Manuel Porcar & Juli Peretó (2014) 1st edition, Springer.
Synthetic Biology (2 Volumes). Robert A. Meyers (2015) 1st edition, Blackwell Verlag GmbH.
An Introduction to Systems Biology: Design Principles of Biological Circuits, Uri Alon (2019) 2nd edition, Chapman and Hall/CRC.
Software
CellDesigner: A modeling tool of biochemical networks (http://www.celldesigner.org)
Course groups and languages
The information provided is provisional until November 30. After this date, you will be able to consult the language of each group through this link. To access the information, you will need to enter the course CODE