General information

Course type AMUPIE
Module title Structure of macromolecules
Language English
Module lecturer prof. UAM dr hab. Szymon Krzywda
Lecturer's email szymon@amu.edu.pl
Lecturer position prof. UAM, dr hab.
Faculty Faculty of Chemistry
Semester 2026/2027 (winter)
Duration 45
ECTS 5
USOS code ?

Timetable

wykład 15h + ćwiczenia 30h = 45h

Module aim (aims)

  1. Gaining knowledge about symmetry of crystals and molecules including symmetry of viruses.
  2. Understanding the structure of: components of nucleic acids and proteins, nucleic acids, protein folds and macromolecular complexes.
  3. Exercise spatial imagination with an emphasis on understanding the three-dimensional structure of macromolecules and principles governing their construction.
  4. Gaining knowledge about modern methods of macromolecule crystallization.
  5. Acquiring skills to build models of components and nucleic acid fragments, secondary structures of proteins, and simple modeling of the structure of macromolecules.
  6. The ability to use global information resources on the structure of macromolecules.
  7. Ability to assess the quality of the macromolecular model; sensitivity to matters of scientific reliability.
  8. Ability to prepare and deliver a seminar on aspects of macromolecule structure.

Pre-requisites in terms of knowledge, skills and social competences (where relevant)

Basic course of organic chemistry or biochemistry.

Syllabus

Lectures

    1. Symmetry in the world of molecules and crystals.
    2. Principles of protein structure.
    3. Classification of protein folds.
    4. Anatomy and taxonomy of nucleic acids and macromolecular complexes.
    5. Structures of giants: viruses and ribosomes.
    6. Overview of experimental methods of structural biology.
    7. Protein handling and crystallization.
    8. Electron density maps and model building.
    9. Macromolecule Data Banks and model validation.
    10. Perspectives of macromolecule crystallography.

      Practicals

      • Symmetry, point & space groups, international notation, enantiomorphism and stereoscopy.
      • Amino acids, hydrogen bonds, building models of amino acid side chains.
      • Protein and DNA model building - construction of models of protein secondary structure and B-DNA (two practicals).
      • Electron density maps and their interpretation.
      • Protein structure refinement and validation.
      • PDB and bioinformatics tools for protein analysis.
      • Analysis of protein structure using Kinemage molecular graphics.
      • Analysis of the catalytic mechanism of HIV-1 protease and its inhibition by possible drug against AIDS.
      • Seminars on the structures of macromolecules, e.g., the polio virus.

Reading list