Biochemistry

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Credits
6
Types
Compulsory
Requirements
This subject has not requirements
Department
UPF;UB
Mail
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

  • Silvia Busquets Rius ( )

Others

  • Maria Isabel Hernández Alvarez ( )
  • Rubén Cereijo Téllez ( )

Weekly hours

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

Learning Outcomes

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: C6, K1, S6,
  2. To use the appropriate tools to obtain information, design experiments, and interpret the results of biochemical processes.
    Related competences: K6, S6, S9, C7, S8,

Contents

  1. Structure of Proteins
    1.1 Structure of Proteins
    Amino acids and peptide bond.
    Primary, secondary, tertiary, and quaternary structure.
    Native and denatured structure.

    1.2 Protein Folding
    Protein folding, involved forces
  2. Enzymes and Enzyme Kinetics
    2.1. Enzymes
    Concept of enzymatic activity. Measurement. Units of enzymatic activity (kat and U.I.). Specific activity. Turnover number.
    Specificity (substrate and reaction specificity).
    Active site. Concept of catalytic, binding, conformational, and non-essential residues.
    Nomenclature and classification of enzymes (classes and main subclasses). Cofactors. Basic concepts (holoenzyme and apoenzyme). Inorganic cofactors. Organic cofactors (coenzymes): cosubstrates and prosthetic groups. Vitamins. Redox coenzymes (NAD and FAD) and group transfer coenzymes.
    General mechanisms of catalysis: proximity and orientation. Induced fit.

    2.2. Enzyme Kinetics and Regulation
    Chemical kinetics (reaction order and 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. Significance of Kcat, KM, and KS. Efficiency index of an enzyme.
    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.
  3. Bioenergetics
    Free energy.
    Endergonic and exergonic reactions. Energy coupling.
    Structure of ATP. Orthophosphate and pyrophosphate hydrolysis.
    Substrate-level phosphorylation. Functions of ATP. Energy charge.
    Redox potential. Conjugate redox pairs.
    Relationship between redox potential and free energy.
  4. Electron Transport Chain and Oxidative Phosphorylation
    Localization and structure of the components of the electron transport chain.
    Chemiosmotic theory of oxidative phosphorylation. Sites of phosphorylation. P/O ratio.
    Energy efficiency of the electron transport chain.
    Coupling and uncoupling. ATP synthase. Respiratory control.
  5. Protein synthesis and degradation
    5.1. 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.
    5.2. Protein translation
    Initiation, elongation, and termination of translation. Differences between prokaryotes and eukaryotes.
    Energetic and kinetic considerations of protein synthesis.
    5.3. Post-translational modifications
    Post-translational modifications of proteins.
    Glycoconjugates and lipoprotein conjugates.
    5.4. Protein degradation
    Protein turnover.
    Lysosomal mechanisms. Autophagy.
    Cytosolic mechanisms: Calpains. UPS and Ubiquitin.
  6. Metabolism
    6.1. Introduction to metabolism
    Anabolism and catabolism. Types of metabolic reactions.
    Transport of metabolites.
    Food digestion.
    6.2. Carbohydrate metabolism
    Uptake and transport of glucose.
    Glycolysis.
    Fermentations.
    Pentose phosphate pathway.
    Gluconeogenesis.
    Glycogenesis and glycogenolysis.
    6.3. 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.
    6.4. 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.
    6.5. Nitrogen metabolism
    Catabolism of amino acids. Fate of amino group nitrogen. Urea cycle.
    Anabolism of amino acids. Biogenic amines.

Activities

Activity Evaluation act


Theoretical expository lectures


Objectives: 1
Contents:
Theory
27h
Problems
0h
Laboratory
0h
Guided learning
0h
Autonomous learning
0h

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.

There will be an oral presentation of a project assigned during the problem-solving sessions.

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.
Oral presentation: 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. The 10% from the oral presentation is not considered.
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. Oral presentation is not required.
Synthesis test: 90%.

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

Bibliography

Basic:

Web links