Molecular Manipulation and Biotechnology

Code:

BIO3002

Acronym:

BIO3002

Keywords
Classification	Keyword
CNAEF	Biology and Biochemistry

Instance: 2023/2024 - 1S

Active?	Yes
Responsible unit:	Department of Biology
Course/CS Responsible:	Bachelor in Forest Engineering and Biotechnology

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
L:EBF	3	Official Study Plan	3	-	6	42	162

Teaching language

Suitable for English-speaking students

Objectives

Provide basic concepts on recombinant DNA technologies, cloning and their applications in the genetic transformation of organisms, with a view to obtaining recombinant proteins. Familiarization with technical approaches, concrete problems and specific vocabulary. Use of basic bioinformatics tools in experimental planning to obtain recombinant proteins (sequence analysis using databases - NCBI -, BLAST, alignments and homology searches, annotation programs). Laboratory practice focusing on cloning reporter genes into expression vectors. Familiarization with experimental design logic and data analysis.
Basic principles of biotechnology: classical or traditional biotechnology, and modern molecular biotechnology. Examples of how Biotechnology is applied in the development of products in different areas (Agriculture, Biofuels, Medicine). Providing basic concepts related to synthetic biology and the main areas of research.

Learning outcomes and competences

Understanding of the experimental logic for the production of recombinant proteins and the underlying molecular processes such as regulation of gene expression. Knowledge of the DNA sequencing and molecular manipulation techniques involved in the production of recombinant proteins.

Acquisition of basic skills in the "in silico" design of parts, synthetic modules based on an understanding of the underlying molecular processes, namely the regulation of gene expression.

 Acquisition of laboratory skills in the preparation and analysis of restriction plasmid DNA, agarose gel electrophoresis. Acquisition of basic bioinformatics skills, namely database searching and sequence analysis and annotation.

Working method

B-learning

Program

Sequence analysis and bioinformatics tools. DNA cloning - Restriction enzymes and other enzymes for DNA manipulation. DNA cloning strategies. Plasmids and other cloning vectors. Antibiotics as selection markers. Alpha-complementation and insertion inactivation. The lac promoter. DNA sequencing. Next generation sequencing (NGS).
Review of basic concepts in Molecular Biology (namely the processes of transcription and translation). Introduction to synthetic biology. Concept of a standardized biological part (bio-lego) and codon optimization. Database and repository of biological parts, and construction of modules and circuits. Requirements for chassis organisms. Main areas of research in Synthetic Biology. Examples of modification of genetic/metabolic pathways with a view to specific applications. BioModularH2, Cyanofactory and PhotoBioCat projects as case studies.

The role of plant biotechnology in plant breeding (marker-assisted selection - MAS, quantitative trait loci - QTLs). Biotechnological approaches to disease control. Genetically modified plants.

Laboratory classes: Basic biosafety rules and handling of laboratory material. Plasmid DNA extraction and DNA electrophoresis on agarose gel. Characteristics and maps of plasmid vectors (selection markers). Molecular markers. Analysis of restriction maps.

Mandatory literature

Videira, A ; Engenharia genética – Princípios e aplicações

Complementary Bibliography

Glick, Bernard R. and Patten, Cheryl L; Molecular Biotechnology: Principles and Applications of Recombinant DNA,, American Society for Microbiology, 2017
Micklos DA, Freyer GA ; DNA Science: A First Course
Watson, J. D., Caudy, A. A., Myers, R. M. & Witkowski, J. A; ) Recombinant DNA. Genes and genomes: a short course
Watson James D. 1928- 070; Recombinant DNA. ISBN: 9781429203128
Sambrook Joseph; Molecular cloning. ISBN: 978-087969-577-4 (Vol. 1)

Teaching methods and learning activities

Online lectures of an expository nature using images/animations and constant encouragement of active participation by students. The use of real research examples provides the context of reality and allows students to acquire the notion that science is a constant search for answers.
Practical laboratory classes following on from the subjects covered in the lectures, and with well-defined objectives of introducing specific DNA manipulation and cloning techniques. Problem-solving (online classes).

Software

Primer3
pDRAW32
Serial cloner
NEB cutter

keywords

Natural sciences > Biological sciences > Biological engineering > Genetic engineering
Natural sciences > Biological sciences > Biology > Molecular biology

Evaluation Type

Distributed evaluation without final exam

Assessment Components

designation	Weight (%)
Exame	100,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Estudo autónomo	114,00
Frequência das aulas	48,00
Total:	162,00

Eligibility for exams

Calculation formula of final grade

The assessment will consist of two tests. The tests will cover the subject matter of the theoretical and practical classes and each one will be graded on a 0-20 scale.

Final grade= (test1 + test2)/2

It is possible to take a make up exam covering the whole subject (theory and practical), in the "Época de Recurso".

Classification improvement

Grade improvement can be made until the time of the make up exams of the academic year subsequent to the one in which the student obtained approval. It can therefore be done by tests (if taken during the normal exam period) or by a global test (if taken during the make up exam period).