Biochemistry

Credits
6
Types
Compulsory
Requirements
This subject has not requirements , but it has got previous capacities
Department
UPF;UB
Mail
silviabusquets@ub.edu
This course covers fundamental concepts and topics in Biochemistry, from the basic molecules of life to methabolism and molecular biology methods. The course covers from the structure and function proteins and cellular components to cell metabolism.

Teachers

Person in charge

Others

Weekly hours

Theory
2
Problems
1.5
Laboratory
0.5
Guided learning
0
Autonomous learning
6

Competences

Learning Outcomes

Knowledge

  • K1 - Recognize the basic principles of biology, from cellular to organism scale, and how these are related to current knowledge in the fields of bioinformatics, data analysis, and machine learning; thus achieving an interdisciplinary vision with special emphasis on biomedical applications.
  • K6 - Recognize the ethical problems that arise from advances in the knowledge and in the application of biological concepts and their computational processing.

    • Skills

  • S6 - Identify and interpret relevant data, within the area of study, to make judgments that include social, scientific or ethical reflections.
  • S8 - Make decisions, and defend them with arguments, in the resolution of problems in the areas of biology, as well as, within the appropriate fields, health sciences, computer sciences and experimental sciences.
  • S9 - Exploit biological and biomedical information to transform it into knowledge; in particular, extract and analyze information from databases to solve new biological and biomedical problems.

    • Competences

  • C6 - Detect deficiencies in the own knowledge and overcome them through critical reflection and the choice of the best action to expand this knowledge.
  • C7 - Detect, from within the scope of the degree, inequalities based on sex and gender in society; integrate the different needs and preferences based on sex and gender in the design of solutions and problem solving.

    • Objectives

    1. Acquisition of the basic knowledge of Biochemistry (Biomolecules and Metabolism)
      Related competences: K1, S6, C6,
    2. To use the appropriate tools to obtain information, design experiments, and interpret the results of biochemical processes.
      Related competences: K6, S6, S8, S9, C7,

    Contents

    1. Structure of Proteins
      Structure of Proteins. Amino acids and peptide bond. Primary, secondary, tertiary, and quaternary structure. Native and denatured structure.
      Protein Folding. Protein folding, involved forces.
    2. Protein synthesis and degradation.
      Transmission of genetic information in protein synthesis. Transmission of genetic information: nucleic acids and the central dogma of molecular biology. Genetic code: Degeneracy. Machinery required for protein translation: Ribosomes, tRNA, aminoacyl-tRNA synthetases.
      Protein translation. Initiation, elongation, and termination of translation. Differences between prokaryotes and eukaryotes. Energetic and kinetic considerations of protein synthesis.
      Post-translational modifications. Post-translational modifications of proteins. Glycoconjugates and lipoconjugates.
      Protein degradation. Protein turnover. Lysosomal mechanisms. Autophagy.
      Cytosolic mechanisms: Calpains. UPS and Ubiquitin.
    3. Characteristics of enzymes
      Characteristics of enzymes. Cofactors: Nomenclature and classification of enzymes. Classes and main subclasses. Active site. Catalytic, binding, conformational, and non-essential residues. Activation energy and transition state. Binding energy. General mechanisms of catalysis. Specific catalytic mechanisms: Acid-base catalysis; Covalent catalysis; Metalloenzymes.
    4. Enzyme kinetics and regulation.
      Enzyme kinetics and regulation. Chemical kinetics (reaction order and the concept of rate constant). Measurement. Initial velocity.
      Michaelis-Menten and Haldane-Briggs equations. Derivation of the equation. Kinetic parameters (KM and Vmax): Meaning and units. Meaning of Kcat, KM, and KS. Enzyme efficiency index.
      Graphical representations. Linearizations (Lineweaver-Burk and Eadie-Hofstee).
      Inhibition of enzymatic activity. Irreversible. Reversible: types (competitive, non-competitive, and uncompetitive). Graphical representations. Meaning and calculation of KI.
    5. Electron Transport Chain and Oxidative Phosphorylation
      Electron Transport Chain and Oxidative Phosphorylation. Localization and structure of the components of the electron transport chain. Chemiosmotic theory of oxidative phosphorylation. Phosphorylation sites. P/O ratio. Structure of ATP. Orthophosphate and pyrophosphate hydrolysis. Substrate-level phosphorylation. Functions of ATP. Energy efficiency of the electron transport chain. Coupling and uncoupling. ATP synthase. Respiratory control.
    6. Introduction to metabolism
      Introduction to metabolism. Anabolism and catabolism. Types of metabolic reactions. Transport of metabolites. Food digestion.
    7. Carbohydrate metabolism
      Carbohydrate metabolism. Uptake and transport of glucose. Glycolysis. Fermentations. Pentose phosphate pathway. Gluconeogenesis. Glycogenesis and glycogenolysis.
    8. Major pathways of oxidative metabolism
      Major pathways of oxidative metabolism. Acetyl-CoA and pyruvate dehydrogenase complex (PDH). Citric acid cycle (Krebs cycle). Overview and reactions. Anaplerotic pathways. Amphibolic nature of the citric acid cycle. Mitochondrial transporters.
    9. Lipid metabolism
      Lipid metabolism. Lipids and lipoproteins. Lipolysis. Fatty acids: Transport, uptake, and activation. ß-oxidation. Ketone bodies: Synthesis and degradation. Lipid synthesis: Lipogenesis, fatty acid esterification, and cholesterol synthesis.
    10. Nitrogen metabolism
      Nitrogen metabolism. Catabolism of amino acids. Fate of amino group nitrogen. Urea cycle. Anabolism of amino acids. Biogenic amines.

    Activities

    Activity Evaluation act



    Bioinformatics seminars: exercises and computational work


    Objectives: 2
    Theory
    0h
    Problems
    20h
    Laboratory
    0h
    Guided learning
    0h
    Autonomous learning
    0h

    Laboratory practices

    To determine the specific activity of Lactate Dehydrogenase (LDH) in a liver homogenate sample: 1. Determine the enzymatic activity of LDH in the liver homogenate. 2. Determine the kinetic parameters Vmax and Km of LDH for the substrate pyruvate, in different dilutions of liver homogenate and in the presence of an inhibitor.
    Objectives: 2
    Theory
    0h
    Problems
    0h
    Laboratory
    8h
    Guided learning
    0h
    Autonomous learning
    0h

    Independent Learning Hours



    Theory
    0h
    Problems
    0h
    Laboratory
    0h
    Guided learning
    0h
    Autonomous learning
    90h

    Mid term exam



    Theory
    0h
    Problems
    2h
    Laboratory
    0h
    Guided learning
    0h
    Autonomous learning
    0h

    Synthesis test



    Theory
    3h
    Problems
    0h
    Laboratory
    0h
    Guided learning
    0h
    Autonomous learning
    0h

    Teaching methodology

    The course will combine face-to-face sessions (theory and exercises) and practical laboratory sessions.

    Specifically, the subject consists of:

    Lectures: full group and split group.
    Bioinformatics problem-solving classes: split group.
    Laboratory practices: two sessions of four hours each in the laboratory, conducted in both team and individual settings, 8 hours.

    Mid exam: two hours.
    Synthesis test: three hours.

    Evaluation methodology

    Assessment:

    Theoretical and practical knowledge acquired will be evaluated. Attitude in various course activities is also assessed. Attendance to practical sessions is mandatory for evaluation. Exception: Repeat students who have already completed the practicals do not need to repeat them.

    Continuous assessment:

    Mid exam: 40%.
    Synthesis test: 40%.
    Practical questionnaire: 10%. Question included in the synthesis test.
    Problem evaluation: 10%.
    A minimum of 5 out of 10 points is required to pass the course.

    The Mid exam is eliminatory.

    Reassessment:

    Open to anyone who has failed or did not attend the assessment.
    No minimum grade requirement.
    Comprehensive exam. Practical score is retained.
    A minimum of 5 out of 10 points is required to pass the course.

    Single assessment:
    Theoretical and practical knowledge acquired, as well as interest and attitude in various course activities, will be evaluated. Attendance to practical sessions is mandatory for evaluation. Exception: Repeat students who have already completed the practicals do not need to repeat them.
    Practical questionnaire: 10%. Question included in the synthesis test.
    Synthesis test: 90%.

    Copying in any exam or plagiarizing in an essay results in failing the course.

    Bibliography

    Basic

    Web links