autumn 2022
KJE-3402 Protein Structure - 10 ECTS
Course content
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.Objectives 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
Information to incoming exchange students
This course is open for inbound exchange student who meets the admission requirements, including prerequisites. Please see the Admission requirements" and the "Prerequisite" sections for more information.
Do you have questions about this module? Please check the following website to contact the course coordinator for exchange students at the faculty: https://en.uit.no/education/art?p_document_id=510412
Examination
| Examination: | Date: | Duration: | Grade scale: |
|---|---|---|---|
| School exam | 30.11.2022 09:00 |
4 Hours | A–E, fail F |
Coursework requirements:To take an examination, the student must have passed the following coursework requirements: |
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| Practical exercises and approved report | Approved – not approved | ||
- About the course
- Campus: Tromsø |
- ECTS: 10
- Course code: KJE-3402
- Responsible unit
- Department of Chemistry
- Contact persons
-
Hanna-Kirsti Schrøder Leiros
Professor, Biomolecular and Structural Chemistry, Norstruct
+4777645706
hanna-kirsti.leiros@uit.no -
Renate Lie Larsen
Senior executive officer, student administration, purchaser, Department of Chemistry,
+4777644074
renate.larsen@uit.no -
Bjørn Olav Brandsdal
Professor, Theoretical and Computational Chemistry, Hylleraas Centre for Quantum Molecular Sciences
+4777644057
bjorn-olav.brandsdal@uit.no
- Earlier years and semesters for this topic