Module Title

Physical Biochemistry

Degree Programme:

Learning Outcomes

After completion of the course, students should be able to

• Understand the relevance of theoretical concepts to the biosciences.
• Understand where various equations of physical biochemistry come from.
• Understand the link between theory and experiment.
• Able to perform simple but realistic calculations.

Lecturer(s):

• André Juffer: Lectures.
• Teaching assistants: Satyan Sharma, Leonardo Garma: Workshops
• Tutors: Anja Konzack, Eveliina Halmetojo, Arna Raasakka.

Program:

• Lectures and workshops (exercises with home work). Main topics:
  • Thermodynamics
  • Equilibrium
  • Protein-ligand association.
  • Acid and bases, acid dissociation constants (pK_as).
  • Protein folding
  • Chemical kinetics, enzymology
• NO FINAL EXAMINATION. Final grade is based upon Workshops.

Recommended Text Book(s):

• Price NC et al., Principles and problems in Physical chemistry for Biochemists, Third edition, Oxford University Press, Oxford, 2001.
• Atkins P and De Paula J, Physical chemistry, 8ed, Oxford University Press, Oxford, 2006.
• Atkins P and de Paula J. Physical chemistry for the life science, Oxford University Press, Oxford, 2006.

Lecture Notes (PDF and OpenOffice Calc/Microsoft Excel)

• Introduction (PDF)
• Basic mathematics (PDF)
• Concepts of thermodynamics (PDF)
• Equilibrium (PDF)
  • Van 't Hoff isochore (Microsoft Excel / OpenOffice Calc) | Van 't Hoff isochore (PDF)
• Protein - ligand (PDF)
  • Dissociation constant single binding site (Microsoft Excel / OpenOffice Calc) | Dissociation constant single binding site (PDF)
  • Dissociation constant inhibitor, number of binding sites (Microsoft Excel / OpenOffice Calc) | Dissociation constant inhibitor, number of binding sites (PDF)
  • Hill coefficient (Microsoft Excel / OpenOffice Calc) | Hill coefficient (PDF)
• Acid and bases (PDF)
  • Titration curve and charge state (Microsoft Excel / OpenOffice Calc) | Titration curve and charge state (PDF)
  • Protein titration curve and pI | Protein titration curve and pI (PDF)
• Protein folding (PDF)
• Chemical kinetics (PDF)
  • Rate determination, example 1 (Microsoft Excel / OpenOffice Calc) | Rate determination, example 1 (PDF) |
  • Rate determination, example 2 (Microsoft Excel / OpenOffice Calc) | Rate determination, example 2 (PDF) |
• Enzyme kinetics (PDF)
  • Enzyme kinetics analysis (Microsoft Excel / OpenOffice Calc) | Enzyme kinetics analysis (PDF)

Lectures

Remaining Lectures schedule

• April 23, 14:00-16:00h, BK122
• April 24, 14:00-16:00h, BF119A

Workshops

Workshops and Tutoring schedule

• April 5: Tutoring session (8-10 am).
• April 11: Mathematics and thermodynamics: Homework, Extra Questions
• April 16: Equilibrium: Homework, Extra Questions
• April 20: Tutoring session (9-11 am)
• April 20: Acid-base and protein folding : Homework, Extra Questions
• May 2: Tutoring session (9-11 am), ROOM: TF103
• May 2: Kinetics: Homework,y Extra Questions
• May 3,4: Excel workshops (two groups).