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 by 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).

We will also discuss what consequences protein knowledge has on society and how old and new knowledge on proteins will influence society in the future. This is coupled to the UN sustainability goals, i.e. how protein science can help humanity obtain better health, clean energy, innovation, stopping climate change and safeguarding life on land and in the sea.

The lectures start 4-6 weeks before the exercises, in order to give the necessary theoretical background. Full-day exercises once per week with a teacher present. It is strongly advised to participate in an active way in the computer exercise since this is of paramount importance for understanding the topics.

It should be emphasized that this course is intended for master's degree students and requires the ability to work independently in the field using computers and the internet.

The course also contains a practical computerlab course that teaches the students how to analyze protein sequences and structures using protein bioinformatic techniques commonly used. There will be focus on learning the 'PyMol' software, which is used to analyze and visualize 3D protein structures. The students will learn how to identify functional regions of the proteins structures as well as how to visualize their findings via informative (and advanced) graphics and animations.

The students will gain experience in how to prepare and deliver effective oral and written presentations of technical information and scientific results. For this purpose, the students will preapre a semester assignment in the form of a digital documentary/story. They will learn to think critically and solve complex problems, as well as learn to accurately 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.
• Can derive functional information for a protein by analyzing its three-dimensional structure.
• Can make good and informative figures of protein structures and sequence alignments
• Can write an illustrated academic text OR create a digital story about a given topic within protein chemistry.
• Can 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 1) how proteins affect all forms of life 2) how protein function has evolved 3) how to develop and use proteins for industrial use 4) 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.