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General Biochemistry B

Objectives

Aims:

After the course it is expected that the students know the basic structural features of the major biological macromolecules and understand the physical-chemical principles underlying the relationship between structure and function. The students should also understand the strategy, regulation, and bioenergetics of the central metabolic pathway. It is expected that the students apply the concepts developed in the lectures to the analysis of experimental results obtained in the laboratory classes and to problem solving.

At the end of this course the student should:

  • understand the structural organization and composition of proteins;
  • know the techniques used in the purification and characterization of proteins and how to evaluate the efficiency of a purification process;
  • understanding the mechanisms of oxygen transport/storage by hemoglobin and myoglobin and distinguish between cooperative and uncooperative interaction;
  • using mathematical models, to calculate the kinetic parameters of Michaelis-Menten enzymes in the absence and presence of inhibitors, and evaluate the effect of temperature and pH on the reaction rate;
  • know the structures of simple sugars and polysaccharides;
  • Understand the structure of nucleic acids and their physicochemical properties; the flow of genetic information from gene to protein;
  • be aware of the structures of lipids and their organization; biological membranes and biological transport;
  • Understand metabolism and bioenergetics: central metabolic pathway and ATP synthesis (glycolysis and gluconeogenesis, the citric acid cycle, electron transport chain and ATPS synthesis)

General characterization

Code

7321

Credits

6.0

Responsible teacher

José Luís Capelo Martinez

Hours

Weekly - 4

Total - 58

Teaching language

Português

Prerequisites

Strongly recommended a basic background of organic chemistry and general chemistry.

Bibliography

 Main Book: Medical Biochemistry. Fourth edition.

JohnW. baynes and Marek H. Dominiczak

Saunders Elsevier.

 

PRINCIPLES OF BIOCHEMISTRY
Voet, D., Voet, J.G. & Pratt, C.W.
John Wiley & Sons, Inc., New York, 3rd ed. 2008

BIOCHEMISTRY
Lubert Stryer
W. H. Freeman and Company, San Francisco. 6th Ed. 2007

 

LEHNINGER PRINCIPLES OF BIOCHEMISTRY
Nelson, D.L., & Cox, M.M.
W.H. Freeman and Company, San Francisco, 5th ed. 2008

Teaching method

Lectures (02:00, 14 weeks) and theoretical-practical lessons (03:00, 4 weeks), with the help of slides in Powerpoint; the talks are part of the teaching programme and the discussion and resolution of problems and questions are about matters of discipline. Laboratory sessions and seminars (03:00, 5 weeks) in groups of 3 to 4 students.

The concepts developed in the lectures are applies to the analysis of the experimental results obtained in the laboratory and to problem solving in the TP classes. The preparation of the working sessions andlaboratory classes is an important part of the work inautonomy by the student, but is subject to review and correction by the teacher.

Evaluation method

Assessment Regulations and Course Requirements

It is recommended to read the Faculty''s assessment regulations:
http://www.fct.unl.pt/sites/default/files/Reg_Aval.pdf

Assessment

The assessment consists of both practical and theoretical components. The final grade will be calculated using the following formula:

Final Grade = (0.80 × Theoretical Grade) + (0.20 × Practical Grade)

Students will pass the course with a final grade of 9.5 or higher. There is no minimum grade required for any individual test, but the average of the five tests (four theoretical + one practical) must be at least 9.5 to pass the course.

IMPORTANT

  • During the exam, students are strictly prohibited from speaking to anyone except the instructor(s) present in the exam room. Any exchange of comments between students will result in immediate expulsion from the exam room, and the exam will be graded as 0 (zero).

  • During classes, all electronic devices must be turned off. Mobile phones, tablets, and computers must not have an active connection. Failure to comply with this rule will result in the student''s expulsion from the classroom.

  • The PDF materials provided are guidelines for studying and do not serve as a comprehensive biochemistry textbook. Students are strongly encouraged to use the PDFs as reference guides and expand their knowledge using the recommended bibliography.

Course Attendance Requirements

  1. Mandatory attendance of all five laboratory practical sessions.

    • Punctuality, preparation, and execution of laboratory work contribute to obtaining attendance certification.

  2. Mandatory attendance of at least 70% of theoretical lectures and 70% of theoretical-practical sessions (only applicable to first-time enrolled students).

Theoretical Grade Calculation

  • Continuous assessment through three tests (1 hour each).
  • To pass the course, the average grade of the three tests must be at least 9.5.

Practical Grade Calculation

  • One test after completing all laboratory sessions.
  • There is no minimum grade required for the practical component.
  • The practical grade obtained in the previous academic year remains valid for the current year.

Important Notes

  • The grades for all tests will be rounded to one decimal place.

  • The final theoretical and practical grades will also be rounded to one decimal place before applying the final grade formula.

  • Students who have already obtained attendance certification in previous years are exempt from practical sessions.

  • For repeating students, the final grade will be calculated as:
    Final Grade = Theoretical Grade (without the practical component).

  • Improvement of the final grade can be achieved through a final exam covering both theoretical and practical components.

  • If deemed necessary by the instructor, an oral exam may be required for grade justification.

Subject matter

Syllabus

  1. Introduction to Biochemistry (Biological structures, metabolic pathways, expression and transmission of genetic information). 
  2. The amino acids properties: peptide bonds - Classification and characteristics. Acid-base properties
  3. Levels of protein structure organization: primary, secondary (alpha helices, beta sheets and other structural elements), tertiary and quaternary structures. Protein isolation, purification and sequencing.
  4. Mass spectrometry of proteins.
  5. Structure-function mechanisms.
  6. Enzyme kinetics Inhibition and regulation. 
  7. Carbohydrates (Classification and function). Monosaccharides and structural and storage polysaccharides (cellulose, chitin, starch and glycogen). Glycoproteins (Proteoglycans and glycosylated proteins). 
  8. Biological Membranes: structure and dynamic. Biological transport: Passive-mediated transport, active-transport. Ion channels, Uniport, symport, and antiporte systems. 
  9. Nucleic acids (RNA and DNA): structure and function. Denaturation and Renaturation of nucleic acid. 
  10. Metabolism (Catabolism and anabolism) and Bioenergetics: Glycolysis, lactic and alcoholic fermentation, Citric acid Cycle, electron transport chain and oxidative phosphorylation.

Problem-solving sessions

  1. Amino acid and proteins – Acid-base properties 
  2. Separation methods in biochemistry
  3. Enzymes and enzymatic kinetics
  4. Nucleic acids. Lipids and biological membranes. Biological transport.
  5. Metabolism and bioenergetics

Laboratory sessions

5 laboratory sessions:

  • Ion-Exchange Chromatography

  • Size-Exclusion Chromatography

  • Protein Quantification

  • Lactase Kinetics


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