Systems Biology and Bioprocesses

Code:

BIOL4057

Acronym:

BIOL4057

Level:

400

Keywords
Classification	Keyword
OFICIAL	Biology

Instance: 2022/2023 - 2S

Active?	Yes
Responsible unit:	Department of Biology
Course/CS Responsible:	Master in Applications in Biotechnology and Synthetic Biology

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
M:ABBS	22	The study plan from 2019/20	1	-	6	42	162

Teaching language

Portuguese

Objectives

Basic conccepts of System's Biology and Bioprocesses will be presented and discussed, trying as much as possible to frame them within appropriate case studies.The competences aquired will form  the basis for future work in research and development labs, as well as in industrial environements, forming important basis for future insertion in different labou market areas (food industry, pharmaceutical, cosmetics).

Learning outcomes and competences

The content of the course integrate concepts of biochemistry, biophysics and engineering as applied to bioprocesses and systems biology.
It is expected that by the end of the UC the students are familiar with the cntent and applications of  bioprocesses and systems biology, as well as their importance and advantages as compared to more classical approaches.

The introduction of case studies, that will be presented mainly as results of individual student's litterature search should provide them an aditional practical dimansion, that is foreseen as very important as regarding their future employability is the target areas, from research to industrial applications.

Working method

Presencial

Program

1. Bioprocesses - definition, scope, exemplres. Kinetics and thermodynamics of micro-organism's methabolism.

2. Reaction kinetics in bioprocesses.
Kinetics - revise previous basic concepts. Kinetics in biological context. Enzymes, the biological atalists. Kinetics of enzymatic reactions involving one singe substrate. Mechanism of Michaëlis-Menten. Catalystic eficiency. Mecanisms of ordered and disordered complex. Ping-pong mechanism. Enzymatic inhibition - copmpetitive, non-competitive and  anti-competiitve. Equations and graphic representation.

3. Thermodynamis of biological processes.
Energetics of ative transport.ATP as mediator of biological energy transfer.

4. Energy balances
Fundamentals for the calculation of mass balances; open vs closed systems; stady and non-steady states. Mono and multu-phase systems. Different reactor types used in industrial environement.
Transport processes in bio-reactors. Exemple. 'Scale-up' to industrial scale.

5. Bioprocesses - case studies (for the final class, each student presents one, as part of the evaluation process).

6. Systems Biology
The fundamental scales in biology. deterministic modeling of the dynamics of biochemical networks: model formulation; numerical simulation; quais-equilibrium. quasi-steady state functional aproximations; stability and sensitivity analysis; model evaluation. Fundamental concepts in system's theory; properties of recurrent regulatry patterns in biological networks.

Mandatory literature

Pauline Doran; Bioprocess Engineering Principles. ISBN: 978-0-12-220851-5
Nelson Lima, Manuela Mota;; Biotecnologia- Fundamentos e Aplicações, 2003. ISBN: ISBN 972-757-197-2

Complementary Bibliography

Sarfaraz K. Niazi, Justin L. Brown; 1. Fundamentals of Modern Bioprocessing , CRC Press, 2017. ISBN: Justin L. Brown

Teaching methods and learning activities

The tutorials will encompass subject presentation by the lecturers, problem solving, in some cases using computer programs, and case study presentations.

The students will present each a final presentation on a individual case study (from litterature research) or any other theme that will be agreed with the lecturers.

Software

COPASI

Evaluation Type

Distributed evaluation without final exam

Assessment Components

designation	Weight (%)
Apresentação/discussão de um trabalho científico	100,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Estudo autónomo	80,00
Frequência das aulas	42,00
Apresentação/discussão de um trabalho científico	40,00
Total:	162,00

Eligibility for exams

Frequency acquisition

Class attendance, according to the FCUP regulations.

Calculation formula of final grade

The stident will do two individual orsal presentations, one for Bioprocesses (NBP) and another for Systems' Biology (NBS). The final grade will be the average of the classifications obtained in the two, as 

NF = 0.50*NBP + 0.50 * NBS

Special assessment (TE, DA, ...)

The students with special status, ghat do not satisfy the required attendance of the course, will have to do an individual assesment.
In these cases, the fianl grandin is the grading obtainned in this evaluation process.

Classification improvement

Due to the presential type of teaching, to improve grading the student has to follow the course again in a following year.