69162 - Chemical Structures Of Biological System

Learning outcomes

At the end of the courses the student will get the theoretical basis for understanding the relationship between the molecular structure of enzymes and the biochemical reactions catalyzed by them, particularly regarding the bioinorganic aspects of metal-enzymes and metallo-proteins. He will be able to acquire information, including those of spectroscopy nature, necessary to evaluate the chemical changes in the structure of molecules within the food.

Course contents

• Primary structure of proteins and chemical-physical properties of their constituting amino acids
• Secondary structure and Ramachandran plot
• Prosthetic groups, apo and holo-protein
• Sequence homology and maintenance of biological function
• Description and use of bioinformatics programs for validation of protein structures (molmol and CLUSTALX)
• NMR parameters and information on the chemical nature of biological systems
• RX crystallography and NMR spectroscopy for the elucidation of the structures
• Metal ions abundance in nature and in biological fluids
• Uptake of metal ions in the cells
• Transferrin, siderophores and Chaperones
• Enterobactin and competitive inhibition of ferric-MECAM
• Principles of chemical kinetics and Arrhenius law
• Michaelis-Menten kinetics and saturation
• Hints on Hard-Soft theory
• Dissociation constants and affinity
• Defining the catalytic site and mechanisms of enzymatic reactions
• Metal ions and effect of coordination on the acidic constant of water
• Role of metal ions in hydrolytic enzymes
• Mechanism of action of carboxy peptidase and carbonic anhydrase
• Conformational flexibility and stability
• Transduction of the chemical signal into mechanical energy: contractile proteins
• Structural differences between hemoglobin and myoglobin and their implications in their different physiological function
• Electronic state of iron ions in the high and low spin
• NMR of myoglobin and adducts with cyanide
• Paramagnetic effect on the chemical shift of NMR signals
• Nuclear relaxation of the water protons: interaction with paramagnetic ions
• Water redox properties: potential for oxygen reduction and of the H+ ion
• Role of the metal ion (Fe or Cu) and optimal coordination geometries in electronic transport
• Role of the geometry of the ligands on E0 of plastocyanin and azzurine
• Redox potential of the proteins and pathways of electron transfer
• Frank-Condon effect and Marcus theory
• Catalytic mechanism of superoxide dismutase

Readings/Bibliography

Scientific papers on authoritative journals
Bioinorganic Chemistry - I. Bertini, H.B. Gray, S.J. Lippard, J.S. Valentine (Eds.) -University Science Books, Mill Valley, CA, U.S.A., ISBN: 0935702571

Teaching methods

The teaching consists of 4 ECTS. Each ECTS includes 6 hours of lectures and 4 hours of practical work in class. The practical work is carried out in the Computer Laboratory at the Campus of Cesena (Villa Almerici) with 20 PC workstations with access to the network. Students will follow the operations conducted by the teacher through the overhead screen projection. The objective of the practical exercises is twofold:
- Have the student familiar with the bioinformatic tools for the analysis of structural data
- To develop the student's ability to independently develop hypotheses on the relationships between structure and function of biological molecules

Assessment methods

The examination at the end of the course aims to assess the achievement of learning objectives:
- Using the information provided in class to develop hypotheses on the structural characteristics of macromolecules
- Describing, with properties of language and scientific rigour, the mechanisms of function for some emblematic enzymes
- Defining the criteria by which the effects of the chemical environment on the function of biological molecules can be evaluated

     For the examination, the student could chose between either a written test or the autonomous preparation of a report accompanied by a PowerPoint presentation.
     1) The written test consists of answering questions concerning the course program, through the description of structural and spectroscopic data which will be delivered to the student during the exam. Subsequently, the student who passes the written test argues orally with the teacher the contents of the assignment in order to reach the final evaluation.
    2) The report and the PowerPoint presentation will be prepared at home by the student on a topic of her/his choice, among those listed in the program, and based on the autonomous elaboration of literature data and on the structural information acquired through the use of the software taught in class.

Teaching tools

The didactic material projected during classes is made available to the student in electronic format. To get educational materials visit the website: http://www.francescocapozzi.it
The freeware softwares "ClustalX" and "MolMol" is available for downloading from the teacher website.
Audio recordings of the lectures is permitted, provided that they are made ​​available to all students through the sharing of mp3 files into restricted areas of the above teacher's website.
Username and password are reserved for students enrolled in the course and is released by the teacher, at the beginning of the course, directly in class. Otherwise, they will be communicated by subscribing to the corresponding mail distribution list.
Public databases for proteins are made accessible via internet.

Office hours

See the website of Francesco Capozzi