Biochemistry I

Code:

Q2014

Acronym:

Q2014

Level:

200

Keywords
Classification	Keyword
OFICIAL	Chemistry

Instance: 2019/2020 - 1S

Active?	Yes
Responsible unit:	Molecular Biology
Course/CS Responsible:	Bachelor in Biochemistry

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
L:BQ	84	Official Study Plan	2	-	6	42	162

Teaching language

Portuguese

Objectives

Acquiring knowledge about the structure of the major classes of biological molecules: proteins, nucleic acids, carbohydrates and lipids and their relationship to biological function.

 Understanding the mechanistic aspects of metabolic reactions in which different compounds are involved.

Acquisition of basic knowledge of some methodologies for the study of different biological molecules.

Learning outcomes and competences

Students acquire capabilities to:

- identify structural characteristics of basic units constituents of different molecular classes namely proteins, carboidrates, and lipids,

-establish relationships between structural characteristics and the phyco-chemistry properties and function of those molecules;

- to know most common methods of isolation and analysis of the biological molecules;

-understand the relevance of regulation at the molecular level for metabolic and also pathophysiologic  processes.

 

 

 

Working method

Presencial

Pre-requirements (prior knowledge) and co-requirements (common knowledge)

The students should have basic knowledge of cellular biology and chemistry, mainly equilibrium, kinetics and termodynamics. The students should aldso have or acquire simultaneously basic knowledge of organic chemistry: main reactive groups and reactivity.

Program

1.    PROTEINS: STRUCTURE AND PROPERTIES

Amino acids basic structure, its classification according to the lateral chains.

Characteristics of the peptide bond.  Peptides and acid-base properties.  Isoelectric point. Intermolecular covalente bonds: dissulfide and Schiff bases. Some examples of biologic relevant  peptides.

Determination of protein primary structure.   Protein sequencing by the Edman method. Chemical and enzymatic proteolysis – peptide maps. Secondary structure: alpha-helix and beta pleated  sheet. Topologies and stabilizing residues.Protein tertiary and quaternary structures.

Globular and fibrous proteins, factors determining protein stability. Structural and functional classification of most common globular proteins. Some fibrous proteins: keratins, collagen and elastina.

Protein isolation and analysis techniques: differential precipitation, chromatography and electrophoresis. . High performance chromatography (HPLC). Strategies for protein purification. Native (PAGE)  and denaturing (SDS-PAGE) electrophoresis systems. Isoelectric focusing.  Immunologic methods for protein identification and quantification. Proteomic studies – bidimensional analysis (2-D) and mass spectrometry.

2. PROTEIN STRUCTURE AND FUNCTION RELATIONSHIPS: MYOGLOBIN AND HEMOGLOBIN AS MODEL

Myoglobin tridimensional structure and the relevance of intramolecular interactions on coformation stabilization.  Heme structure and its localization in the protein. Oxygen binding to myoglobin (hyperbolic curve).

Structural similarities between myoglobin and hemoglobin polypeptide chains. Tetrameric structure of Hemoglobin. Oxygen binding to hemoglobina (sigmoidal curve). Allosteric behaviour of hemoglobin. Regulation of oxygen binding to hemoglobin (Bohr effect).

Hemoglobin variants – sickle cell anemia as an example.

3. PROTEIN-LIGAND INTERACTIONS

Basic concepts of protein-ligand interactions. Determination of dissociation constant using the Langmuir isotherm (one binding site). Scatchard equation (non-cooperative binding)and Hill equation (cooperative interaction). Saturation and competition studies.

4. ENZYMES

Basic structural characteristrics of enzymes.  Substrate specificity. Active center – fixed and inducible center. Factors responsible for the enzymatic catalytic efficiency: orientation and proximity; conformational factors. General acid-base catalysis, covalent catalysis. Some examples of enzymatic catalysis mechanisms: Serine proteases – Chymotrypsin.

Regulation of the enzymmatic activity by covalent modification of specific residues. Regulation by proteolysis. Allosteric regulation.

Some examples of enzymatic mechanisms: phosphofrutokinase, glycogen phosphorylase, aspartyate transcarbamoylase and pyruvate dehydrogenase complex.

5. COENZYMES

Coenzymes as hydrossoluble vitamins. Examples. Role of coenzymes in enzymatic activity.

Coenzymes in redox recations. Mechanisms of action of NAD+ and FAD.

Reactions involving acyl transfer – coenzyme A and lipolysin.

Reactions involving carbonil groups – thiamin.

Transfer of carboxylic groups  - biotin action.

Participation of pyridoxal phpsphate in transamination reactions.

Multienzymatic complexes – keto acids decarboxylation.

 

6. CARBOHYDRATES

Most common mono and disacharides. Characteristics of the structural polysacharides (cellulose and chitin) and of storage polysaccharides (starch and glycogen).

Structure and function of glycosaminoglycans.  The peptidoglycan from the bacterial Wall. Proeopglycans structure and function as components of the glicocalix.

Glycoproteins structure. Relevance of sugar residues in protein structure and function.

Methods for the analysis of sugars, glycosidases activity aand isolation based on lechtin chromatography.

7. NUCLEIC ACIDS

Structure and characteristics of purine and pyrimidine bases. Nucleosides and nucleotides.

DNA double strand: the Watson and Crick model  and A, B and Z strand conformations. Stabilization factors in the DNA structure. DNA denaturation and renaturation.

Structural characteristics of RNA. Susceptibility to alcali hydrolysis. Structural characteristics specific to different RNA types: messenger, transfer, ribosomal and small nuclear RNAs.

Protein-nucleic acids complexes. Associação de ácidos nucleicos a proteínas.

Nucleic acids Isolation and analysis methods. Endonucleases activity. Polymorphisms detection using restriction enzymes.  Polymerase chain reaction –applications in mutation detection.

8. LIPIDS

Structure and physico-chemical properties of fatty acids, triglycerides and phospholipids. Biological function. Sphingolipids: sphingosin , ceramides phosphor and glycosphingolipids –cerebrosides and gangliosides. Prostaglandins.

Isopren the basic unit of  isoprenoids and steroids. Liposoluble vitamins. Steroids structure and function: cholesterol, steroid hormonesand bile acids.

Methods for the isolation and characterization of lipids.

Lipoproteins and their function on lipid transport.

 Biological membranes composition and effects on function modulation. 

Mandatory literature

David L. Nelson, Michael M. Cox; Lehninger Principles of Biochemistry, Macmillan learning, 2013. ISBN: ISBN-10: 1-4292-3414-8; ISBN-13: 978-1-4292-3414-6

Complementary Bibliography

Jeremy M. Berg , John L. Tymoczko, Gregory J. Gatto Jr. , Lubert Stryer ; Biochemistry, Macmillan learning, 2015. ISBN: ISBN-10: 1-4641-2610-0
Andrea T. Da Poian Miguel Castanho; Integrative Human Biochemistry A Textbook for Medical Biochemistry, Springer-Verlag New York, 2015. ISBN: ISBN 978-1-4939-3058-6
,A. Quintas, A.P. Freire, M. J. Halpern; Bioquimica - Organização Molecular da Vida, LIDEL, 2008
Zubay Geoffrey; Biochemistry
Voet Donald; Biochemistry

Comments from the literature

Books indicated exist in the library catalogue. In some cases there are already more updated editions that would be prefered.

Teaching methods and learning activities

- Lectures accompanied by powerpoint presentation. Reference to research projects and results as examples of aplications of the topics studied. Molecular basis of some dieases, in particular involving alterations of protein structure and function.

Refernce to applications in industry and pharmaceutic approaches of some biochemical processes referred to. Resoltuion of exercises during classes.

Students make oral presentations, in groups, under the topics of the program in order to expand their knowledge and detail some topics on biochemistry.  This allows also to develop their ability to work in a group, to organize their knowledge and to comunicate science.

keywords

Natural sciences > Biological sciences > Biology > Molecular biology
Natural sciences > Biological sciences > Biology > Structural biology
Natural sciences > Biological sciences > Biology > Functional biology

Evaluation Type

Distributed evaluation with final exam

Assessment Components

Designation	Weight (%)
Exame	85,00
Prova oral	15,00
Total:	100,00

Amount of time allocated to each course unit

Designation	Time (hours)
Apresentação/discussão de um trabalho científico	30,00
Estudo autónomo	108,00
Frequência das aulas	42,00
Total:	180,00

Eligibility for exams

Conditions of Frequency: must attend the lectures.

To obtain approval, students must obtain a final classification equal or superior to 10 (scale 0-20).

Assessement: continuous evaluation mainly by evaluation of oral presentation and final exam (The final examination is constituted by one part (50%) of multiple choice questions, and another part (50%) of the more elaborate answer questions.. 

Calculation formula of final grade

The final evaluation is calculated considering   a contribution of 85%  (0-20) of the final exam and continuous assessment (oral presentation) contributes 15% (0-20), 

Since oral presentation in groups is opctional students that do not make it are evaluated only by the classification obtained in the final exam.

 Valuation formula:  85% (theoretical final exam) + 15% (oral presentation). The theory test can not be rated less than 7.0 (7/20).

Students that do not make  oral presentation  will be evaluated only from the final exam that will have a supplementary section for evaluation.

Examinations or Special Assignments

Not applicable.

Internship work/project

Not applicable.