Biophysics and Biochemistry

Code:

MA221

Acronym:

BB

Keywords
Classification	Keyword
OFICIAL	Biophysics and Biochemistry

Instance: 2014/2015 - 2S

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	43	Plan 2012 to 2017	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:
Proteins – Protein structure. Determination of the structure of proteins: experimental techniques of atomic resolution and low resolution.
Membranes (transport) – Membrane potential and electrochemical gradient. Passive transport of ions; structure and function of protein channels. Active transport of ions; structure and function of the sodium-potassium, protons and calcium pumps.
Nerve conduction – basis aspects of electricity. Action potential. Transmission of electric impulses in axons.
Oxidative phosphorylation. Description of the process. Structure, function and energy efficiency of the ATP-synthase. Inhibitors and uncouplers of oxidative phosphorylation.
Oxidative stress - Reactive oxygen species, molecular damages and antioxidant defences.
Carbohydrate metabolism – Glycolysis and lactic acid fermentation. Glycogen metabolism and gluconeogenesis. The pentose-phosphate pathway. Integration and 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.
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 glycerophospholipids and sphingolipids. Biosynthesis of cholesterol. Primary and secondary bile acids. Steroid hormones. 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 and nitric oxide.
Nucleotide metabolism – Synthesis of purines and pyrimidines. Inhibitors of nucleotide biosynthesis and replication. Catabolism of purines and pyrimidines.

Practical classes
1. Protein crystallization
2. Observation of diffraction phenomena – applications of Bragg’s law.
3. Visualization of structural models of macromolecules.
4. Techniques of subcellular fractionation: homogenisation of tissues and cells; differential and isopycnic centrifugation.
5. Protein purification techniques: differential precipitation; chromatography; electrophoresis. Assessing the degree of purity.
6. 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, at the end, make a small report. The report focus on the presentation of the results and their interpretation. 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

Distributed evaluation with final exam

Assessment Components

Designation	Weight (%)
Exame	85,00
Trabalho laboratorial	15,00
Total:	100,00

Eligibility for exams

In accordance with the law: presence in 2/3 of the practical classrooms.

Written exam > 10 (out of 20).

Calculation formula of final grade

Classification of practical evaluation (15%) + classification of written exam (85%)

Examinations or Special Assignments

Not applicable

Special assessment (TE, DA, ...)

As specified by the Pedagogic council

Classification improvement

As specified by the Pedagogic council