KJB310 Protein Chemistry
Showing course contents for the educational year 2022 - 2023 .
Course responsible: Gustav Vaaje-Kolstad
Teachers: Vincentius Gerardus Henricus Eijsink
ECTS credits: 10
Faculty: Faculty of Chemistry, Biotechnology and Food Science
Teaching language: EN, NO
Limits of class size:
Teaching exam periods:
This course starts in Autumn parallel. This course has teaching/evaluation in Autumn parallel.
Course frequency: Annually
First time: Study year 2004-2005
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 work on what consequences protein knowledge has influenced 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. The exercises are one full day 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.
Basic knowledge in bioinformatics and use of computers is an advantage.
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.
To pass KJB310 the candidate must obtain an approved semester assignment and obtain the grade E or better on the final written exam.
After completion of KJB310 protein chemistry, the candidate will have the following learning outcomes:
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.
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.
When one has completed and passed the 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.
Lectures, some with group exercises.Weekly exercises with a teacher present, in which students work in pairs on a computer, using databases and analysis tools available on the Internet and on the local computer.Compulsory semester exercise; either writing a article for "Store Norske Leksikon" or make a digital story about a selected topic.
Questioning hours will be organized right before the exam.Two teachers will be available for questions during the weekly exercises.Lecture notes will be available in Canvas.
Arthur M. Lesk: Introduction to Protein Science, Oxford University Press, Third Edition, 2016LecturesCourse bookletSemester exercise
Biochemistry equivalent to KJB200.
Bioinformatics equivalent to BIN210. Biochemistry laboratory course, equivalent to KJB201.
Approved semester assignment.
An approved semester assignment is valid for 2 years.
Written examination, 3.5 hours, counts 100 %.
- Lectures: 35 hours.
- Exercises: 30 hours.
- Semester assignment: 20 hours.
- Individual study: 165 hours.
Total: 250 hours
Special requirements in Science
Reduction of credits:
There is some overlap with BIN210, this does not reduce the number of credits earned, however.
Type of course:
Per normal week:
4 hours lectures 5 hours exercise.
An external examiner approves the examination questions and marks a minimum of 25 selected examination papers.
Allowed examination aids: A1 No calculator, no other aids
Examination details: One written exam: Letter grades