Biostructures Modelling

Code:

Q3009

Acronym:

Q3009

Level:

300

Keywords
Classification	Keyword
OFICIAL	Chemistry

Instance: 2019/2020 - 1S

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	18	study plan from 2016/17	3	-	6	56	162

Teaching language

Suitable for English-speaking students

Objectives

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.

- will be able to describe the structure and properties of all the amino acids that include the natural proteins.

- will be familiar with the molecular structure of proteins and the 3D motifs they adopt at each level of structure organization.

- students will be able to describe all kinds of functions of proteins in living organisms.

- students will understand that protein structure is related to function.

- students will understand the basic principles of catalytic action of enzymes and their interaction with substrates.

- students will be able to describe the molecular structure of DNA and the basis of replication.

- students will be able to understand a few common interactions between DNA and proteins.

- 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. 

- students will be familiar with the PDB-Protein Data Bank and with the necessary computational tools to retrieve information from it.

- students will be able to manipulate protein molecular models within the specific software VMD-Visual Molecular Dynamics. 

Working method

Presencial

Program

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. Visualization and manipulation of proteins in silico.
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 visualization and manipulation of molecular models in silico (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

Mike Williamson; How Proteins Work, Garland Science, 2012. ISBN: 978-0-8153-4446-9

Complementary Bibliography

John Kuriyan; Boyana Konforti; David Wemmer; The Molecules of Life, Garland Science, 2012. ISBN: 978-0-8153-4188-8
Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter; Molecular Biology of the Cell, 5th ed., Garland Science, 2007. ISBN: 9780815341062

Comments from the literature

Other supporting material will be provided at Moodle platform.

Teaching methods and learning activities

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

Software

Amber e VMD

keywords

Physical sciences > Chemistry > Computational chemistry

Evaluation Type

Distributed evaluation with final exam

Assessment Components

designation	Weight (%)
Exame	50,00
Teste	25,00
Trabalho escrito	25,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Estudo autónomo	28,00
Frequência das aulas	48,00
Trabalho escrito	8,00
Total:	84,00

Eligibility for exams

The students must attend at least 75% of the time in classroom.

Calculation formula of final grade

Final grade =50%PM + 50%EX
PM- arithmetic mean of the practical test and the final project.
EX- Final Theoretical Exam.
Neither mark (PM and EX) should be less than 7,0 ( in 20 ).

Examinations or Special Assignments

.

Special assessment (TE, DA, ...)

.

Classification improvement

Only the theoretical component of the classification can be improved by repeating the final exam.