Høst 2022

KJE-3402 Protein Structure - 10 stp

The course is administrated by

Institutt for kjemi

Type of course

Theoretical and practical subject. The course is available as a singular or elective course independent of study program, also to exchange students. The course is offered on condition that a minimum number of students register for the course.

Course overlap

KJE-8402 Protein structures 10 stp

Course contents

Of all molecules in a living organism, the proteins have the most diverse functions and due to this, they are also the most complex molecules in a cell. Their function is closely related to the complex 3D structure and the course focuses on this close relationship. The course is an introduction to the basic principles of protein structure, including the properties of amino acids, secondary structure elements, motifs, folds, classification based on fold and the relation between 3-dimensional structure and function of proteins. Intramolecular forces like hydrogen bonds, ionic and van der Waals interactions are extensively covered. The basic principles of the hydrophobic effect are also included. Basic properties of the amino acids in a protein such as H-binding, pKa, size, shape, polarity and secondary structure propensities are covered. The general principles of secondary structure elements and motif are extensively covered by the syllabus of the course. The students are furthermore expected to learn how the 3D-structure of a protein determines the function. This is taught through a detailed discussion of a series of protein classes; enzymes, DNA-binding and DNA-modifying proteins, receptors, membrane bound signalling proteins, proteins active in the immune system, virus proteins and the fibre type of proteins. Factors affecting the stability of a protein are discussed for all parts of the course. Some important methods for structure determination (X-ray crystallography and NMR), along with basic modelling techniques are also discussed. The content and use of some of the most important databases for protein structure data are examined both theoretically and through hands-on exercises.

Application deadline

Applicants from Nordic countries: 1 June for the autumn semester

Exchange students and Fulbright students: 15 April for the autumn semester.

Admission requirements

Formal prerequisites:

A bachelor degree in chemistry, biochemistry or equivalent, with a grade C or better in the Norwegian grading system.

Objective of the course

The student will have acquired a solid and broad theoretical basis to understand protein structure. This means that the student:

Knowledge:

Properties of amino acids

has extensive knowledge about the molecular structure of the natural amino acids
has in-depth knowledge about the chemical and structural properties of the individual amino acids both in their free form and in a protein
has insight into the properties of the peptide and the peptide bond and how these properties influence the folding and structure of a protein
has knowledge about the main intramolecular forces involved in the stabilization of proteins; their origin, magnitude and role in proteins

Structural hierarchy and structural diversity

has knowledge about the main structural levels in proteins; primary, secondary, tertiary and quaternary
has insight into how structural elements like secondary structures, motives and folds are built and stabilized
knows about and can distinguish between globular, membrane bound and fiber proteins and can relate the classes to structural features
has knowledge about classification of proteins based on both function and structure
has insight into the main functional protein classes and has detailed knowledge about structure-function relationships for typical example proteins for every functional class

Binding sites and intramolecular interactions

has knowledge about general mechanisms for ligand binding and intermolecular interactions; enzymes active sites and enzyme catalysis, antibody binding sites, protein-DNA interactions, receptor binding responses in signalling etc.

Methods for obtaining structural information

knows the most important techniques for determination and analyses of 3-dimentional structures at atomic resolutions; their major strengths and limitations and the interpretation of deposited structural information in the relevant data banks

Skills:

can describe the properties of the amino acids, peptides, secondary structure elements and motifs, and are able to evaluate their impact and role at various placements in a protein structure
can outline in details the structure and stabilizing factors of frequently occurring secondary structure elements, motives and folds
can describe key features of proteins belonging to various functional classes in general terms and describe such features specifically for example proteins for each functional class
has acquired the basic knowledge to understand how the atomic resolved protein structure is determined and is able to sketch and understand the main steps in the procedure for determine structures by the use of NMR and X-ray crystallography
can outline the main steps in a molecular modelling procedure and understands the pitfalls and limitations of a modelled structure
can interpret and manipulate electronic three-dimensional models from a PDB file

Competence:

understands the relation between chemical/structural properties of a protein and the function, and can use this knowledge to discuss and interpret structure-function relations
has the ability to read and understand in general terms, research papers where the structure-function relationships of a protein are discussed

Language of instruction

The language of instruction and examination is English and all of the syllabus material is in English.

Teaching methods

Lectures: 28 h, Seminars: 8 h, Laboratory: 30 h PC-based exercises

Date for examination

School exam 30.11.2022

The date for the exam can be changed. The final date will be announced at your faculty early in May and early in November.