Høst 2017

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 3-D 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.

Admission requirements

Students should have basic knowledge in organic chemistry and biochemistry.

Objective of the course

The candidate..

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 Peptide and peptide bond
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 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
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.

Language of instruction

The language of instruction is English and all of the syllabus material is in English. Examination questions will be given in English, and may be answered in either English or a Norwegian/Scandinavian language.

Teaching methods

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

Assessment

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

Date for examination

Written test 24.11.2017

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