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: Archive

Comment

01016601 (former UVA) is identical with this course description. 
The course can not be followed by students who have passed KE523 Physical chemistry. 

Entry requirements

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

Content

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.

See Blackboard for syllabus lists and additional literature references.

Examination regulations

Prerequisites for participating in the exam a)

Timing

Autumn

Tests

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.

EKA

N200019112

Assessment

Second examiner: None

Grading

Pass/Fail

Identification

Student Identification Card

Language

Normally, the same as teaching language

Examination aids

To be announced during the course 

ECTS value

0

Additional information

The prerequisite examination is a prerequisite for participation in exam element a).

Exam element a)

Timing

January

Prerequisites

Type Prerequisite name Prerequisite course
Examination part Prerequisites for participating in the exam a) N200019101, BMB540: Physical Biochemistry

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

Examination aids

Not allowed, a closer description of the exam rules will be posted under 'Course Information' on Blackboard.

ECTS value

5

Additional information

The examination form for re-examination may be different from the exam form at the regular exam.

Indicative number of lessons

48 hours per semester

Teaching Method

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

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.


Teacher responsible

Name E-mail Department
Daniel Wüstner wuestner@bmb.sdu.dk
Himanshu Khandelia hkhandel@sdu.dk

Timetable

Administrative Unit

Biokemi og Molekylær Biologi

Team at Educational Law & Registration

NAT

Offered in

Odense

Recommended course of study

Profile Education Semester Offer period