KJE-8402 Protein structures - 10 stp

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 3-D structure and the course focuses on this close relationship.

The course covers 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.

Registration deadline for PhD students at UiT - The Arctic University of Norway: September 1st

Application deadline for external applicants: June 1st

PhD students or holders of a Norwegian master´s degree of five years or 3+ 2 years (or equivalent) may be admitted. PhD students must upload a document from their university stating that there are registered PhD students. This group of applicants does not have to prove English proficiency and are exempt from semester fee.

Holders of a Master´s degree must upload a Master´s Diploma with Diploma Supplement / English translation of the diploma. Applicants from listed countries must document proficiency in English. To find out if this applies to you see the following list:

Proficiency in English must be documented - list of countries

For more information on accepted English proficiency tests and scores, as well as exemptions from the English proficiency tests, please see the following document:

Proficiency in english - PhD level studies

Students should have some knowledge in organic and biological chemistry and biochemistry.

PhD students at UiT The Arctic University of Norway register for the course through StudentWeb . 

External applicants apply for admission through SøknadsWeb. 

All external applicants have to attach a confirmation of their status as a PhD student from their home institution. Students who hold a Master of Science degree, but are not yet enrolled as a PhD-student have to attach a copy of their master's degree diploma. These students are also required to pay the semester fee.

More information regarding PhD courses at the Faculty of Science and Technology is found here.

The candidate..

Knowledge

Properties of amino acids and peptides

• 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 profound insight into the properties of the peptide and the peptide bond and how these properties influence the folding and structure of a protein

Intramolecular forces

• Has in-depth 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 good  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 well 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 extensive knowledge about 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 extensively 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
• Are able 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

General 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.

A final written exam, 4h. Lettergrades (A-F).

Coursework requirements: Five practical exercises and approved report.

There will not be arranged a re-sit exam for this course.

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