BMB540: Physical Biochemistry
Study Board of Science
Teaching language: Danish or English depending on the teacher, but English if international students are enrolled
EKA: N200019112, N200019102
Assessment: Second examiner: None, Second examiner: Internal
Grading: Pass/Fail, 7-point grading scale
Offered in: Odense
Offered in: Autumn
Level: Bachelor
STADS ID (UVA): N200019101
ECTS value: 5
Date of Approval: 25-04-2019
Duration: 1 semester
Version: Approved - active
Entry requirements
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
Content
The following main topics are contained in the course:
First part, taught by FKF teacher.
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.
See itslearning for syllabus lists and additional literature references.
Examination regulations
Prerequisites for participating in the exam a)
Timing
Autumn
Tests
Portfolio
EKA
N200019112
Assessment
Second examiner: None
Grading
Pass/Fail
Identification
Full name and SDU username
Language
Normally, the same as teaching language
Examination aids
To be announced during the course
ECTS value
0
Additional information
The examination consists af participation 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 examination is a prerequisite for participation in exam element a).
The prerequisite examination is a prerequisite for participation in exam element a).
Exam element a)
Timing
January
Prerequisites
| Type | Prerequisite name | Prerequisite course |
|---|---|---|
| Prerequisite not found |
Tests
Written exam
EKA
N200019102
Assessment
Second examiner: Internal
Grading
7-point grading scale
Identification
Student Identification Card
Language
Normally, the same as teaching language
Duration
4 hours
Examination aids
The exam is without aids. However, standard build in calculator in Windows/MAC are allowed. It is also allowed to use Maple, Mathematica, Mathcad, MathLab, GeoGebra Apps, R, R-Studio, CAS TI-Nspire, Ms Excel og LibreOffice Calc. WordMat is allowed but not recommended. Use of WordMat is at your own risk and no support is provided for errors caused by the program. Furthermore, it is also allowed to use "ordbogsprogrammet" (the dictionary programme) from http://www.ordbogen.com/ in electronic form. The browser version is not allowed.
Internet is not allowed during the exam. However, you may visit system "DE-Digital Exam".
ECTS value
5
Indicative number of lessons
Teaching Method
At the faculty of science, teaching is organized after the three-phase model ie. intro, training and study phase.
- Intro phase (lectures) - 22 hours
- Training phase: 26 hours, including 18 hours tutorials and 8 hours laboratory
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.
Activities in the studyphase
- Read the book, accompanying and slides from the lectures
- Home assignments
- Laboratory reports