BB2165 Biomolecular Structure and Function 7.5 credits

Biomolekylers struktur och funktion

Structural biology of biomolecules is a cornerstone in modern biotechnology. The principal objective is to provide the students with theoretical and practical knowledge and insight about the foundations of biomolecular structure, and how the structure relates to function. Instructive computer-based exercises and a project based on contemporary cutting edge research offer a teaching concept that is highly interactive and practical in order to increase and deepen the perception and understanding of biomolecular structure-function relationships. You will learn the necessary skills and tools to retrieve, use, understand, and validate structural biology information available in 3D structure databases. You will also develop expertise in using free computational tools to study the interaction of biomacromolecules with ligands and explain the driving force behind their association or binding and able to propose structure from sequence and to validate it.

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Course information

Content and learning outcomes

Course contents *

Structural biology is a young science and research in this area is moving forward rapidly. The course contents ranges from fundamentals in structural biology to contemporary research, and the precise topics are subjects of change to appropriately reflect the research frontier.

• Basics of protein structure (building blocks, intramolecular and intermolecular interactions, levels of protein structure, canonical protein databases) and other relevant biomolecules.

• Concepts of thermodynamics in the context of protein structure, stability and function (e.g. folding, ligand binding, complex formation).

• Central structure-function concepts in biology (e.g. signal transduction, transcription and translation, molecular transport, molecular motors).

• Overview of methods for experimental structure determination of biomolecules (e.g. crystal structure analysis, single particle cryo-electron microscopy, nuclear magnetic resonance); and biophysical methods for characterization (neutron scattering, circular dichroism, electron paramagnetic resonance, infrared spectroscopy, Raman spectroscopy, optical imaging).

• Computational approaches for modeling of biomolecules and related energetics (e.g. homology modeling, molecular dynamics, Monte Carlo, course-grained approach, molecular docking, free energy calculations, entropy calculations).

• Validation and critical analysis of experimentally derived biomolecular structures.

Intended learning outcomes *

  • Describe, formulate, analyze and evaluate fundamental concepts in biomolecular structural biology.
  • Suggest, motivate and discuss strategies for solving problems related to the function and applications of biomolecules in biology and biotechnology from a structural perspective.
  • Based on knowledge and concepts acquired in the course, be able to propose, discuss and evaluate the role of biomolecular structural biology to advance understanding of biological and biotechnological scientific problems.
  • Use computer software tools and relevant databases to generate, visualize, investigate, analyze, evaluate and validate biomolecular structure information and to estimate the free energy change for various macromolecular association process and for binding to small ligands.
  • Evaluate and discuss biomolecular structure from the perspective of contributing to a sustainable development.
  • Design, plan, execute and present in written and oral form an independent project focusing on biomolecular structure and function.
  • Critically evaluate own and others chosen strategies for targeting scientific problems from a biomolecular structure perspective, including assessing published recent advances in the current subject area.

Course Disposition

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Literature and preparations

Specific prerequisites *

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Recommended prerequisites

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Equipment

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Literature

Branden C, and Tooze J., Introduction to Protein Structure, 2nd Ed. Garland Publishing Inc., 1999.

Andrew Leach, Molecular Modeling: Principles and Applications, 2nd Ed. Prentice-Hall.

Handouts and selected articles.

Examination and completion

Grading scale *

A, B, C, D, E, FX, F

Examination *

  • LAB1 - Laboratory work, 1.5 credits, Grading scale: P, F
  • LIT1 - Literature task, 2.0 credits, Grading scale: P, F
  • TEN1 - Examination, 4.0 credits, Grading scale: A, B, C, D, E, FX, F

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

Opportunity to complete the requirements via supplementary examination

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Opportunity to raise an approved grade via renewed examination

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Examiner

Christina Divne

Further information

Course web

Further information about the course can be found on the Course web at the link below. Information on the Course web will later be moved to this site.

Course web BB2165

Offered by

CBH/Industrial Biotechnology

Main field of study *

Biotechnology

Education cycle *

Second cycle

Add-on studies

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Ethical approach *

  • All members of a group are responsible for the group's work.
  • In any assessment, every student shall honestly disclose any help received and sources used.
  • In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.