Syllabus for Structural Bioinformatics

Bioinformatisk strukturbiologi

A revised version of the syllabus is available.

Syllabus

  • 5 credits
  • Course code: 1MB204
  • Education cycle: First cycle
  • Main field(s) of study and in-depth level: Biology G2F, Technology G2F

    Explanation of codes

    The code indicates the education cycle and in-depth level of the course in relation to other courses within the same main field of study according to the requirements for general degrees:

    First cycle

    • G1N: has only upper-secondary level entry requirements
    • G1F: has less than 60 credits in first-cycle course/s as entry requirements
    • G1E: contains specially designed degree project for Higher Education Diploma
    • G2F: has at least 60 credits in first-cycle course/s as entry requirements
    • G2E: has at least 60 credits in first-cycle course/s as entry requirements, contains degree project for Bachelor of Arts/Bachelor of Science
    • GXX: in-depth level of the course cannot be classified

    Second cycle

    • A1N: has only first-cycle course/s as entry requirements
    • A1F: has second-cycle course/s as entry requirements
    • A1E: contains degree project for Master of Arts/Master of Science (60 credits)
    • A2E: contains degree project for Master of Arts/Master of Science (120 credits)
    • AXX: in-depth level of the course cannot be classified

  • Grading system: Fail (U), Pass (3), Pass with credit (4), Pass with distinction (5)
  • Established: 2016-03-08
  • Established by: The Faculty Board of Science and Technology
  • Revised: 2016-04-26
  • Revised by: The Faculty Board of Science and Technology
  • Applies from: Autumn 2016
  • Entry requirements:

    60 credits within the Master Programme in Molecular Biotechnology Engineering, includning Cell Biology and Basic Chemistry.

  • Responsible department: Biology Education Centre

Learning outcomes

After completing the course, the student should be able to

  • account for the structure of proteins, DNA and RNA
  • explain the relationship between protein sequence and protein structure
  • describe how structure translates into function within different biological fields such as catalysis, transport and regulation
  • explain basic principles of experimental methods for the determination of the structure of macromolecules
  • use sequence and structural databases
  • use computer programs to visualise three-dimensional structures and analyse the relationship between structure and function
  • estimate the validity of information in structural databases
  • use bioinformatics tools for sequence alignment, sequence motif identification and prediction of secondary and tertiary structures
  • account for the purpose, theoretical background, ethical aspects and limitations of the above mentioned bioinformatics methods and use this knowledge to interpret relevant results

Content

Structure and characteristics of macromolecules (proteins, DNA, RNA). Relation between sequence, structure and function. Structural basis for the dynamics, binding specificity, catalysis and cooperativity of macromolecules. Function of macromolecules highlighted by a number of examples within fields such as enzymes, membrane proteins, signalling and translation.

Overview of biological databases, servers and information centres. Sequence comparisons. Basic macromolecular structure: three-dimensional structure, PDB co-ordinates, classification of proteins in structure families, programs for analysis and comparison of structures. Introduction to the theory of classification and comparison of sequences and extraction of common distinctive features (e.g., motifs). Sequence analysis for prediction of secondary and tertiary structures, and homology modelling of three-dimensional structures based on sequence data. Research and publication ethics.

Instruction

Lectures, seminars and computer exercises. Attendance at seminars and full participation in computer labs is mandatory to pass the course.

Assessment

Written examination ( 3 credits) , laboratory, exercises and seminars ( 2 credits) .

Syllabus Revisions

Reading list

Reading list

Applies from: Autumn 2016

Some titles may be available electronically through the University library.

  • Petsko, Gregory A.; Ringe, Dagmar. Protein structure and function

    Oxford: Oxford University Press, 2009

    Find in the library

    Mandatory

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