Concepts in Chemical Biology

Course manual 2020/2021

Course content

The ability to critically discuss published data will be trained. After the course, students are expected to know:
- the hallmarks of cancer and know the underlying principles
- core cancer signaling pathways
- inhibition strategies of signaling pathways – e.g. use of small
molecules, stabilized peptides
- peptidomimetics and their use for challenging targets in signaling
pathways
- chemical reactions for the selective covalent modification of proteins
- bio-orthogonal and ligand directed reactions
- classical protein engineering (natural: directed evolution,
disulfide…)
- Biology of the coronavirus life cycle
- SARS antiviral strategies - (non-)natural protein modifications for improved functions - reprogramming of the genetic code

Study materials

Literature

• scientific pubications/reviews will be provided via Canvas

Syllabus

• Introduction
  Mon 29-03-21 @ 11:00 Lecture: General introduction to Chemical Biology also including "How to read a reseach paper and how to prepare a scientific presenation" (via zoom, not recorded)
  1) Targeting Hallmarks of Cancer
  Thu 01-04-21 Lecture (video upload)
  Tue 06-04-21 Deadline for written assignment (7:00 posting, 18:00 deadline)
  Thu 08-04-21 @ 13:30 Group discussion (via zoom, not recorded)

  2) Chemically Advanced Proteins
  Mon 12-04-21 Lecture (video upload)
  Thu 15-04-21 @ 13:30 PyMol Seminar (via zoom, not recorded)
  Fri 16-04-21 Deadline for assignment (video presentation, 12-04 posting, 16-4 18:00 deadline)
  Mon 19-04-21 @ 11:00 Group discussion (via zoom, not recorded)

  3) Coronavirus Biology and Inhibition
  Thu 22-04-21 Lecture (video upload)
  Wed 28-04-21 Deadline for written assignment (10:00 posting, 21:00 deadline)
  Thu 29-04-21 @ 13:30 Group discussion (via zoom, not recorded)

  4) Genetic Code Reprogramming
  Mon 10-05-21 @ 11:00 Lecture (via zoom + video recording and upload)
  Wed 12-05-21 Deadline for assignment (7:00 posting, 18:00 deadline)
  Mon 17-05-21 @ 11:00 Group discussion (via zoom, not recorded)

Objectives

• Students will attain the ability to critically discuss published data
• After the course, students are expected to know the hallmarks of cancer and know the underlying principles
• After the course, students are expected to know core cancer signaling pathways
• After the course, students are expected to know inhibition strategies of signaling pathways – e.g. use of small molecules, stabilized peptides
• After the course, students are expected to know peptidomimetics and their use for challenging targets in signaling pathways
• After the course, students are expected to know chemical reactions for the selective covalent modification of proteins
• After the course, students are expected to know protein labeling techniques (encoded tags, enzymes (PTMs), reactions)
• After the course, students are expected to know bio-orthogonal and ligand directed reactions
• After the course, students are expected to know (non-)natural protein modifications for improved functions
• After the course, students are expected to know classical protein engineering (natural: directed evolution, disulfide…)
• After the course, students are expected to know principles of coronavirus infections
• After the course, students are expected to know the basics of coronavirus targeting approaches

Teaching methods

• Lecture
• Seminar
• Self-study
• Presentation/symposium
• Working independently on e.g. a project or thesis

Audio Lectures: The teacher will upload the teaching content as voice-over power point videos. The students are expected to download the content, watch and familiarize themselves with the content. Additional teaching material for this content (videos, links, pdf of various kinds including research article where appropriate) will be available online (Canvas). Lectures will be given in English. The content of the uploaded voice over power-point lectures and the associated literature are necessary to study carefully in order to be able pass the weekly assignments.

Case Study and Assignment: The students are provided with one or more research papers. In groups of two, questions regarding these case studies are addressed in an assignemnt.

Guided Peer-to-Peer Discussions: In seminar sessions, Peer-to-Peer exchange for each topic will take place. Within these, the students are expected to exchange questions and help each other in answering these. Students are expected to participate actively. Discussions should be held in English and also a joined by one of the lecturers.

Learning activities

Attendance

This programme does not have requirements concerning attendance (TER part B).

Assessment

The course involves four assignments. Each assignment will be performed in groups of two which are assembled randomly by the coordinator and will change for each assignment. Each assignment will be graded and must be passed (grade at least 5.5). The final grade of the course is the average of the four assignments. If a student does not hand in one or more of the assignments, the course is failed. If an assignment is handed in but not passed (grade below 5.5) the students will be have the opportunity for an oral online examination within one week after the assessment. In this case, the student has to contact the course coordinator to make an appointment.

Inspection of assessed work

Direct contact with coordinator.

Assignments

There are four graded group assignments (groups of 1-2):

1) Targeting Hallmarks of Cancer (written)
2) Chemically Advanced Proteins (recorded presentation)
3) Coronavirus Biology and Inhibition (written)
4) Genetic code reprogramming (written)

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Contact information

Coordinator

• T.N. Grossmann