KJB310 Protein Chemistry

The topic «protein chemistry» will give a thorough insight in how proteins function and have developed; how we can study proteins and what makes proteins important for both living organisms and society as a whole. These topics will be covered in the discussion of

• the basics of proteins
• how proteins can be modified after translation
• various methods used for characterization of proteins (with a special focus on methods used to determine protein 3D structure)
• the use of bioinformatic methods to analyze proteins
• how proteins can catalyze chemical reactions (structural determinants, kinetics and reaction mechanisms)
• protein-protein interactions
• evolution and development of proteins and protein function
• protein-related diseases and their mechanisms
• protein folding and how proteins obtain their 3D structure
• how we study proteins in a larger context (systems biology, proteomics).

The course will address the societal implications of our knowledge about proteins to date and how this knowledge can shape the future. This is linked to the UN’s Sustainable Development Goals, including the significance of protein science for good health, clean energy, innovation, halting climate change, and life on land and underwater.

There is a strong emphasis on protein bioinformatics as it has become a very important part of the field. Each lecture on protein bioinformatics will be followed by a 4-hour exercise session where methods explained in the lecture will be practiced. In total, there will be eight practical exercise sessions. Students will learn to analyze protein sequences and three-dimensional protein structures. The tools used are the same as those used by researchers worldwide. There will be a focus on the software "PyMol," which is used to visualize and analyze protein structures. Students will learn to identify functional areas in protein structures and visualize these with informative images and animations. The exercises are crucial for understanding the subject, so it is highly recommended that students actively participate in them.

Students will learn how to prepare and present technical and scientific information. For this purpose, a semester project will be conducted where students will analyze a protein sequence assigned to them during the first protein bioinformatics exercise. They will analyze this sequence using the methods learned during the bioinformatics exercises. In addition to the sequence analysis, students will find scientific literature to help them understand the function of the protein they are analyzing. They will learn to think critically and interpret current research literature.

After completion of KJB310 protein chemistry, the candidate will have the following learning outcomes:

Knowledge

A student who has completed and passed KJB310

• Has deep knowledge of protein building blocks and structure.
• Understands the importance of protein structure for stability and biological activity, and how a protein structure can be determined.
• Understands the background and use of the most common bioinformatic methods used to study the structure and function of proteins.
• Has deep knowledge of different types of proteins and their biological functions.
• Has good understanding of how proteins have developed their properties through evolution and how new functions emerge.
• Understands how proteins achieve their three dimensional structure (protein folding) and what role proteins play in various diseases.
• Understands the interaction between proteins (protein-protein interactions), how this can be investigated and how this affects protein function.
• Understands how enzymes catalyze reactions, how such reactions can be measured and how the results can be analyzed (enzymology).
• Understands and can explain how to improve / modify the properties of proteins using methods such as protein engineering and directed evolution.
• Has a good overview and understanding of the experimental methods that are used to analyze both protein function and structure.
• Has obtained insight into the influence protein science has had and will have on society, with a special focus on relevant sustainability goals.

Skills

A student who has completed and passed KJB310 can

• find functional information about a protein sequence using bioinformatics methods.
• derive functional information for a protein by analyzing its three-dimensional structure.
• make good and informative figures of protein structures and sequence alignments
• write an illustrated academic text OR create a digital story about a given topic within protein chemistry.
• read, understand and critically evaluate academic articles within the field.

General competence

When one has completed and passed KJB310 Protein Chemistry

• One has gained in-depth understanding of how proteins work and can reflect on, among other things
  • how proteins affect all forms of life
  • how protein function has evolved
  • how to develop and use proteins for industrial use
  • which roles proteins play in disease.
• One can judge and critical interpret published scientific papers within the field.
• One is aware of the dangers and pitfalls of protein sequence analysis using bioinformatics.
• One can contribute constructively and creatively in academic discussions and meetings within the field of protein chemistry.
• Knowledge on how to present scientific information using digital tools.