Biophysics and Biochemistry

Code:

MA221

Acronym:

BB

Keywords
Classification	Keyword
OFICIAL	Biophysics and Biochemistry

Instance: 2021/2022 - 3T (of 21-02-2022 to 08-04-2022)

Active?	Yes
Responsible unit:	Molecular Biology
Course/CS Responsible:	Aquatic Sciences

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
LCMA	34	Official Study Plan	2	-	5	49	135

Teaching language

Portuguese

Objectives

The program of Biophysics and Biochemistry aims to prepare students for the understanding of fundamental principles of Physics and its applications in Biology, as well of intermediate metabolism and regulatory mechanisms of metabolic pathways. It is highlighted the importance of signal transduction pathways used by cells to receive, process, amplify and integrate diverse extracellular signals. The student uses basic knowledge to discuss dysfunctions associated with traumas and specific conditions.
This curricular unit also aims at giving students the theoretical and practical knowledge required for the correct utilization of a group of experimental techniques based on physical principles and used for the biochemical characterization of cells, organelles, proteins and metabolites.

Learning outcomes and competences

The student should be able to understand the molecular mechanisms of life in cells. Emphasis will be given to the role of proteins and macromolecules in biochemical processes and to its biophysical characterization either by structure-function and kinetic studies.

Working method

Presencial

Program

Theoretical classes: 

Molecular and Cellular Biophysics

Protein, structure and function.

Electricity. Concept of field and membrane potential. Ion transport across membranes. Ionic protein channels. The nerve axon.

Energy. Oxidative phosphorilation. Electron and proton flux. The ATPsynthase, structure and function.

 

Systems Biophysics

The Physics of Hearing

The Physics of Vision

The Physics of breathing

Fluid mechanics of the circulatory system

Illustrative examples of application of Physics in the living world.

Biochemistry


Carbohydrate metabolism – Glycolysis and lactic acid fermentation. Glycogen metabolism and gluconeogenesis. The pentose-phosphate pathway. Regulation of carbohydrate metabolism. Cellular signalling mechanisms by insulin, glucagon and epinephrine. Metabolic adaptations to starvation. 

Bioenergetics – the complex pyruvate dehydrogenase and the Krebs cycle. Regulation of the Krebs cycle. Amphibolic nature of the Krebs cycle. 
Oxidative stress - Reactive oxygen species, molecular damages and antioxidant defences. 

Lipid metabolism – Digestion and absorption of lipids. Lipolysis and beta-oxidation of fatty acids. Synthesis and energetic role of ketone bodies. Synthesis of fatty acids. Biosynthesis of cholesterol. Lipoproteins. Integration and regulation of lipid metabolism. 

Aminoacid metabolism – Aminotransferases and glutamate dehydrogenase. Biosynthesis of non-essential aminoacids. Catabolism of aminoacids and the urea cycle. Ammonia toxicity. Conversion of aminoacids to specialized products – HEME, melanine, hormones, neurotransmitters, nitric oxide and nucleotides. 

Practical classes:
1. Protein crystallization 
2. Visualization of structural models of macromolecules. 
3. Techniques of subcellular fractionation: homogenisation of tissues and cells; differential centrifugation. 
4. Protein analysis by electrophoresis. 
5. Metabolite analysis and determination of enzymatic activities.

Mandatory literature

Nelson David L.; Lehninger principles of biochemistry. ISBN: 0-7167-4339-6
Thomas M. Devlin; Textbook of Biochemistry with Clinical Correlations, Drexel University School of Medicine, Philadelphia, Pennsylvania, 2006. ISBN: 978-0-471-67808-3
Jeremy M. Berg, John L. Tymoczko, Lubert Stryer; Biochemistry, W. H. Freeman, 2007. ISBN: 0-7167-8724-5
Alexandre Quintas, Ana Ponces Freire, Manuel Halpern; Bioquímica – organização molecular da vida, Lidel – edições técnicas, Lda, 2008. ISBN: 978-972-757-431-5
Sternheim M.M., Kane J.W.; General Physics, John Wiley, N.Y. , 2001. ISBN: 0-471-52278-3

Teaching methods and learning activities

Theoretical classes consist on the presentation of the program content with discussion and resolution of problems/exercises.
In practical classes, students working in groups of two perform the laboratorial work and present and discuss the results obtained. The theoretical bases of the methodologies used are presented by the tutor before the execution of the experiments.

Software

Protein purification (A.G. Booth)

Evaluation Type

Evaluation with final exam

Assessment Components

Designation	Weight (%)
Exame	75,00
Apresentação/discussão de um trabalho científico	15,00
Trabalho laboratorial	10,00
Total:	100,00

Amount of time allocated to each course unit

Designation	Time (hours)
Estudo autónomo	60,00
Frequência das aulas	49,00
Trabalho escrito	26,00
Total:	135,00

Eligibility for exams

According to the rules of the University of Porto: presence in 3/4 of the theoretical-practical classrooms.

Calculation formula of final grade

Classification of written exam (75%).
Oral presentation (15%).
Laboratory work and report (10%)

Examinations or Special Assignments

Students working in groups for presentation/discussion of selected topics

Special assessment (TE, DA, ...)

Special evaluation will be provided to all students with a special status, in a date agreed with the Chair.

Classification improvement

After the completion of the course unit, students can improve their grades. However, they can only improve the grade of the final exam and not the other components (practical evaluation).