Structure and functions of biological macromolecules

biology
chemistry
physics

Basic knowledge of physics, chemistry, and biochemistry is required.

Classroom

Basic biophysical topics of structures, molecular dynamics, and functions of biopolymers, nucleic acids DNA and RNA, proteins, lipids, polysacharides. and their molecular complexes. Detailed problems on physical interactions of biopolymes, thermodynamics of biopolymer systems, and structural analysis of the biomolecules are discussed and trained by means of computers during the classes.

The general aim is to present the basic topics on structure and dynamics of biological macromolecules regarding their functions in the living cell, and according to the paradygm of molecular biophysics and biology, structure - activity -relationship (SAR).

Program:

1. Physical basis of macromolecular structures and interactions, intra- and intermolecular,

- classical energy of a macromoleule; force-field approximation

- thermodynamical description of a macromolecular set in solution (free Gibbs energy),

- molecular conformation and stabilizing contacts: non-bonded electrostatic interactions (hydrogen bonds, salt bridges, van der Waals), hydrophobic interactions, pi-pi stacking and cation-pi stacking, solvent effects,

- recognition specificity of macromolecules in their complexes, dynamical models of the association: induceds fit, fly-casting.

2. General review of biophysical methods: spectroscopy and X-ray diffraction, microscopy, single molecule methods, molecular modelling and structure prediction.

3. Nucleic acids, DNA and RNA:

- DNA replication, transcription, degradation,

- biological role of nucleic acids,

- DNA sequencing,

- scond- and third order structure: helices, loops, tRNA, pseudoknot, A-minor motif, ribose zipper, chromatin and supercoiling.

4. Globular, fibrous, and membrane proteins:

- protein biosynthesis (mRNA translation), topogenesis, degradation,

- biochemical roles,

- sequencing,

- secon-, third-, and fourth-order strusture, Ramachandran plot, domains and their topological classification, subunits,

- protein folding: in silico, in vitro, in vivo,

- protein and RNA enzymes; physical foundations of the enzymatic catalysis,

5. Lipids: membrane structure and dynamics.

6. Polysacharides as structural and storage materials.

7. Macromolecular complexes

8. Molecular biophysics in biotechnology and medicine (selected aspects).

Student's effort:

Lecture = 30 h

Classes = 30 h

Self-studying (2 h per week), ca. 30 h

Preparation to the examination: ca. 20 h

Total, ca. 110 h

Classes Classes are devoted to:

(a) analysis of the intra- and intermolecular interactions including the solvent (classical force field), energy, dynamics and thermodynamics of biomolecules and their complexes;

(b) computer analysis of biopolymer conformations; classification of protein domains and RNA structural motifs.

Description by Ryszard Stolarski, September 2012

1. Genowefa Ślosarek "Biofizyka molekularna" PWN 2011

2. S. Stryer „Biochemistry”

After completion the course:

KNOWLEDGE

1. The student knows actual issues on biopolymer structures and functionality in the living cell..

2. The student knows the physical and chemical bases of biopolymer conformations and interactions.

3. The student knows how structural defects of biological macromolecules result in the meolecular mechanisms of diseases.

SKILLS

1. The student is able to explain the basic phenomena and notions of molecular biophysics.

2. The student is able to use the acquired knowledge on biomolecular structure to explain the biological role of biopolymers.

3. The student is able to apply the basic bioinformatic tools to structural and dynamical analysis of macromolecules.

SOCIAL ABILITIES

1. The student understands development of contemporary biophysics and understands the relating requirements to follow the bibliography of the topic.

2. The student evaluates the application of approximate models to describe properties of macromolecules i regard to biomedical application and practice.

3. The students recognizes ethics in scientific investigationsk.

Final examination in the form of 5 open questions.

Active participation in the classes is taken into account in the final mark.

No