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Computacional Biological Chemistry

Code: Q254     Acronym: Q254

Classification Keyword
OFICIAL Chemistry

Instance: 2014/2015 - 2S Ícone do Moodle

Active? Yes
Responsible unit: Department of Chemistry and Biochemistry
Course/CS Responsible: Bachelor in Chemistry

Cycles of Study/Courses

Acronym No. of Students Study Plan Curricular Years Credits UCN Credits ECTS Contact hours Total Time
L:Q 30 Plano de estudos Oficial 2 - 5 -

Teaching Staff - Responsibilities

Teacher Responsibility
Alexandre Lopes de Magalhães

Teaching - Hours

Theoretical classes: 2,00
Laboratory Practice: 2,00
Type Teacher Classes Hour
Theoretical classes Totals 1 2,00
Alexandre Lopes de Magalhães 2,00
Laboratory Practice Totals 2 4,00
Alexandre Lopes de Magalhães 4,00

Teaching language



The main objectives of this course are:

To study the physical, chemical and biological properties of proteins and DNA.

To know the principles of enzymatic catalysis.

To use computational techniques to study and predict properties of proteins and DNA.

Learning outcomes and competences

- By the end of this course, students will be aware of the fact that fundamental chemical and physical principles also apply to complex biological systems.

- By the end of this course, students will be able to describe the structure and properties of all the amino acids that include the natural proteins.

- By the end of this course, students will be familiar with the molecular structure of proteins and the 3D motifs they adopt at each level of structure organization.

- By the end of this course, students will be able to describe all kinds of functions of proteins in living organisms.

- By the end of this course, students will understand that protein structure is related to function.

- By the end of this course, students will understand the basic principles of catalytic action of enzymes and their interaction with substrates.

- By the end of this course, students will be able to describe the molecular structure of DNA and the basis of replication.

- By the end of this course, students will be able to understand a few common interactions between DNA and proteins.

- By the end of this course, students will be able to understand the basic principles of Molecular Dynamics, to perform simple simulations on small protein systems using the Amber software, and to interpret the results. 

- By the end of this course, students will be familiar with the PDB-Protein Data Bank, and with the necessary computational tools to retrieve information from it.

- By the end of this course, students will be able to manipulate protein molecular models within the specific software VMD-Visual Molecular Dynamics. 

Working method



THEORETICAL CLASSES 1. Molecular interaction in biological systems. 2. Biomolecules- chemistry and structure. 3.From amino acids to Proteins. 4. Primary, Secondary, Tertiary and Quaternary Structure of Proteins 5. Computational Visualization of proteins. 6. Enzymatic Catalysis and Inhibition. 7. Nucleic Acids.

PRACTICAL CLASSES I. Introduction to Linux OS. II. Scientific information and data - PDB (protein databank) - research articles (Web of science) - Web tools to analyze pdb data and structures III. Basics of the visualization of molecules (software VMD) IV. Study and graphical visualization of Amino acids and Proteins V. Molecular Dynamics simulation of the interaction between an enzyme and substrate. (software: Amber ; VMD)

Mandatory literature

Lorraine Buckberry; Paul Teesdale; Essentials of Biological Chemistry, John Wiley & Sons, Ltd, 2001. ISBN: 0-471-48904-2

Complementary Bibliography

John Kuriyan; Boyana Konforti; David Wemmer; The Molecules of Life, Garland Science, 2012. ISBN: 978-0-8153-4188-8
Mike Williamson; How Proteins Work, Garland Science, 2012. ISBN: 978-0-8153-4446-9
Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter; Molecular Biology of the Cell, 5th ed., Garland Science, 2007. ISBN: 9780815341062
Peter Atkins, Julio De Paula; Physical Chemistry for the Life Sciences, Oxford Univ. Press, 2011. ISBN: 978-0-19-956428-6
Hidde Ploegh, Chris A. Kaiser, Angelika Amon, Arnold Berk, Matthew P. Scott, Harvey Lodish, Monty Krieger, Anthony Bretscher; Molecular Cell Biology, 7ed, W.H.Freeman & Co Ltd, 2012. ISBN: 9781464109812

Teaching methods and learning activities

Theoretical lessons complemented with computational sessions using specific software in Linux environment.


Amber e VMD


Physical sciences > Chemistry > Computational chemistry

Evaluation Type

Distributed evaluation with final exam

Assessment Components

designation Weight (%)
Exame 50,00
Participação presencial 0,00
Teste 50,00
Total: 100,00

Amount of time allocated to each course unit

designation Time (hours)
Trabalho laboratorial 12,00
Total: 12,00

Eligibility for exams

The students must attend at least 75% of the practical classes.

Calculation formula of final grade

Final grade =50%PE + 50%EX PE- arithmetic mean of the two practical evaluations planned for the semester. EX- Final Theoretical Exam Both evaluations marks (PE and EX) should not be less than 7,0 ( in 20 ).

Examinations or Special Assignments


Special assessment (TE, DA, ...)


Classification improvement

The student can repeat the final theoretical exam on the date and under the rules defined by the Conselho Pedagógico of the Faculty of Sciences of Porto.

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