autumn 2019

KJE-3402 Protein Structure - 10 ECTS

Sist endret: 10.10.2019

The course is provided by

Faculty of Science and Technology

Location

Tromsø |

Application deadline

Applicants from Nordic countries: 1 June for the autumn semester 

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

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.

Admission requirements

Formal prerequisites:

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

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

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

Assessment

A final 4h written exam counting 100%. Lettergrades A-E, F-Fail.

Coursework requirements: Compulsory attendance for five practical exercises. One approved project report.

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

Date for examination

Written test 25.11.2019

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

Schedule

Course overlap

K-342 Protein structure 6 stp
KJE-8402 Protein structures 10 stp

Recommended reading/syllabus

Pensumliste for KJE-3402 Protein Structure


Kontakt
Profilbilde Renate Lie Larsen

Renate Lie Larsen


Seniorkonsulent, studieadministrasjon, Innkjøper institutt for kjemi,
Telefon: +4777644074 renate.larsen@uit.no

Hanna-Kirsti S.Leiros.jpg

Hanna-Kirsti Schrøder Leiros


Professor, Strukturkjemi, Norstruct
Telefon: +4777645706 hanna-kirsti.leiros@uit.no