BMB540: Physical Biochemistry (5 ECTS)

STADS: 01016601

Level
Bachelor course

Teaching period
The course is offered in the autumn semester.

Teacher responsible
Email: wuestner@bmb.sdu.dk
Email: hkhandel@sdu.dk

Timetable
Show entire timetable
Show personal time table for this course.

Prerequisites:
None

Academic preconditions:
Students taking the course are expected to:

• Have knowledge of first year mathematics including first order differential equations, basic statistics.
• Is able to perform and understand basic integration and differentiation, is able to isolate variables and solve algebraic equations.
• Is familiar with logarithm and exponential functions.
• Be able to use scientific software to solve equations, isolate variables and plot functions in dependence of given parameters.
• Knows basic physical principles of electrodynamics, -statics and optics, as taught at gymnasium-level.
• hav knowledge to chemistry and biochemistry equalling FF503 

Course introduction
The aim of the course is to enable the student to interpret biochemical systems quantitatively, which is important in regard to a deeper understanding of metabolic and genetic regulation of cellular processes. The course will introduce the basic concepts of physical chemistry with applications in classical biochemistry and molecular cell biology.

The course will provide knowledge of physico-chemical principles of bio-macromolecular organization and cell function.

The course builds on the knowledge acquired in the courses listed under academic preconditions below, and gives an academic basis for studying the topics of the bachelor project but also of courses, such as advanced molecular biology and metabolic regulation as well as bioanalytical instrumentation and advanced microscopi, which are part of the degree.

In relation to the competence profile of the degree it is the explicit focus of the course to:

• Give the competence to connect thermodynamic and kinetic concepts with molecular and cellular processes.
• Give skills to be able to analyse biological and biochemical systems from a quantitative standpoint.
• Give knowledge about the quantitative, physical and chemical basis of biochemical systems

Expected learning outcome
The learning objective of the course is that the student demonstrates the ability to:

• calculate changes in Gibbs free energy, entropy and enthalpy in biomolecular processes
• define conditions for spontaneity of chemical reactions and derive the law of mass action
• define properties of mixtures and solutions, such as ion activity and acid-base equilibria
• describe the time evolution of spontaneous processes including chemical kinetics and transition states
• define conditions for a steady state in thermodynamically open systems and calculate steady state fluxes and concentrations
• interpret diffusion from a microscopic and macroscopic viewpoint
• explain the thermodynamic coupling in bioenergetics
• define conditions for feedback loops and oscillations in biochemical processes, as found in metabolism or gene activation
• describe and interpret biochemical binding processes
• explain the principles behind the interaction of light with biomolecules from a classical and quantum mechanical view

Subject overview
The following main topics are contained in the course:
First part, taught by FKF teacher.

• Statistical Thermodynamics and Kinetic theory (for relating microscopic and macroscopic quantities, concept of entropy
• Thermodynamics of ideal gases
• First Law
  • Work, heat, internal energy and enthalpy
  • Thermochemistry: enthalpy of biochemical reactions
• Second Law
  • Entropy, Gibbs Free energy
  • Chemical Potential
• Thermodynamic calculations (Adiabatic, Isotherms, summary of first and second laws etc.)
• Properties of Mixtures and Solutions.
  • Description of mixtures
  • Osmosis and Activity (Real solutions)
  • Ionic solutions, Acid-Base equilibria
  • Biological Interfaces, Surface tension

Second Part, taught by BMB teacher.

• Biochemical kinetics including reaction orders, rate laws, time-scale separation, oscillations and transition to steady state
• Ionic solutions in biochemistry (buffers, protonation states and organelle properties)
• Two-State Systems in Cell Biology exemplified on Binding processes
• Light-matter interactions with basics from quantum mechanics exemplified on processes of biological relevance, such as photo- damage, vision, photosynthesis and fluorescence
• Introduction to diffusion with examples from cell biology

Literature

• John Kuriyan, Boyana Konforti, David Wemmer : The Molecules of Life - Physical and Chemical Principles, ISBN:9780815341888, 1st. edition.
• Peter Atkins, Julio de Paula: Physical chemistry for the life sciences , 2nd edition.

Website
This course uses e-learn (blackboard).

Prerequisites for participating in the exam

1. Paticipation in laboratory exercises and approval of written reports. Internal evaluation by the teacher on a pass/fail basis. Students must get at least ¾ of the assignments apporved. The prerequisite aims at exam a). (01016612).

Assessment and marking:

1. Written exam. Evaluation by internal censorship according to the 7-mark scale. No exam aids are allowed. A closer description of the exam rules will be posted under 'Course Information' on Blackboard. (5 ECTS). (01016602).

Expected working hours
The teaching method is based on three phase model.
Intro phase: 22 hours
Skills training phase: 26 hours, hereof:
 - Tutorials: 18 hours
 - Laboratory exercises: 8 hours

Educational activities

• Read the book, accompanying and slides from the lectures
• Home assignments
• Laboratory reports

Educational form
The lectures introduce the concepts and set the stage for the lab activities in the training phase. The exercises will be primarily used for solving calculation problems. This is in our opinion the best way to allow the students to get familiar with quantitative thinking and the theoretical concepts.

Language
This course is taught in Danish or English, depending on the lecturer. However, if international students participate, the teaching language will always be English.

Remarks
The course can not be followed by students who have passed KE523 Physical chemistry.

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.