Physical and Organic Chemistry

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Credits
6
Types
Compulsory
Requirements
This subject has not requirements, but it has got previous capacities
Department
UB
This course plan ensures students have a comprehensive understanding of Chemistry principles, combining theoretical knowledge with practical problem-solving skills.This course encompasses basic and essential concepts of Chemistry for the subsequent development of many of the subjects that make up the Bioinformatics degree. Some of these concepts may have already been introduced in high school programs. The rest is new material that is covered in a gradual and reasoned manner with the help of problem-solving classes and practical application exercises to highlight the significant usefulness of chemistry and to understand the extent to which it determines or affects the world around us.

Teachers

Person in charge

  • Joan Carles Domingo Pedrol ( )

Others

  • Federica Battistini ( )
  • Josep Lluis Gelpi Buchaca ( )

Weekly hours

Theory
2
Problems
2
Laboratory
0
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.

Objectives

  1. Understanding Chemical Principles of Life and Basic Concepts of Life Chemistry
    Related competences: K1, S8, S9, C6,
  2. Ability to apply knowledge to practice
    Related competences: K6, S6, S8, C6,

Contents

  1. Fundamentals
    Chemistry in Bioinformatics- Elements and atoms. Compounds. Types of chemical compounds and their formulation. Nomenclature and formulation of inorganic compounds. Moles and molar masses. Empirical and molecular formulas. Reactions and chemical equations. Types of chemical reactions and stoichiometry. Limiting reagent and reaction yields. Reactions in aqueous solution. Mixtures and solutions. Types of solutions. Expression of solution concentration.
  2. Atomic Structure and Chemical Bonding
    Constituents of atoms. Atomic nucleus and isotopes. Atomic orbitals and electronic configuration. Types of chemical bonds. Covalent bonding. Lewis formulas. Bond polarity. Molecular geometry: valence bond method and orbital hybridization theory. Intermolecular forces: Van der Waals forces, hydrogen bonds, and hydrophobic interactions.
  3. Chemical Thermodynamics
    Thermodynamic systems. Work, heat, and energy. First law of thermodynamics: internal energy. Processes at constant pressure: enthalpy. Energy in chemical reactions. Reaction heat: Hess's law. Spontaneous processes. Second law of thermodynamics: entropy. Entropy and probability. Absolute entropies and the third law of thermodynamics. Entropy balance of a reaction. Gibbs energy: spontaneity and free energy.
  4. Kinetics and Catalysis
    Reaction rate. Rate laws. Reaction order. Variation of the rate constant with temperature. Arrhenius equation. Activation energy. Collision theory. Transition state theory. Reaction mechanisms. Rate-determining step. Catalysis. Biological catalysts: enzymes.
  5. Chemical Equilibrium
    The concept of equilibrium: equilibrium constants. Expression of equilibrium constants: homogeneous and heterogeneous equilibria. Considerations regarding the equilibrium constant and its mathematical expression. Reaction quotient. Factors affecting chemical equilibrium: Le Châtelier's principle. Relationship between equilibrium constant and free energy of reaction.
  6. Acid-Base Equilibria
    Nature of acids and bases. Arrhenius concept. Brönsted-Lowry concept. Lewis acid-base concept: acid or basic character and electronic structure. Acids and bases in aqueous solution. Strength of an acid or base. Autoionization of water. pH concept. Polyprotic acids and bases.
  7. Oxidation-Reduction Reactions
    Oxidation-reduction reactions: oxidants and reductants. Balancing redox reactions. Galvanic cells. Standard electrode potentials: the electrochemical series. Relative strengths of oxidants and reductants. Nernst equation. Criteria for spontaneous change. Electron transfer in biological systems.
  8. Organic Chemistry and Chemistry of Biomolecules.
    Carbon and organic chemistry, Hybridation and types of CC bonds. Formulas, Structures, Representations, File formats. Types and structure of organic compounds.
  9. Hydrocarbons
    Resonant systems, and Aromatic HCs. Isomery. Esteroisomery. Conformation isomery
  10. Functional groups
    Overall classification and rellevance to biology. Alcohols/Thiols. Cholesterol, Estheroids. Ethers/ThioEthers. Amines. Cyclic Amines. Purines. Pyrimidines. Aldehydes and Ketones. Sugars. Isomery and conformation. Ribose conformation and puckering. Glycosidic Bond and Polyshaccharides. Nucleosides. Carboxylic acids. Fatty acids. Amino Acids. Structures/types. Acid Base issues. Roles in proteins. Esthers/thioesthers. Triglicerids, phospholipids. Nucleotides. Roles in Biology. Rellevant nucleotides (ATP, etc). Phosphodiester bond, Amides. Peptidic bond.
  11. Basic reactivity of organic compounds
    Oxidation/reduction. Redox coenzymes, NAD(P), FMN, FAD. Hydrolysis. Nucleophiles in biology. Group transfer. Phosphorilation/dephosphorilation. Transmination

Activities

Activity Evaluation act




Visualization of molecules


Objectives: 2
Contents:
Theory
0h
Problems
10h
Laboratory
0h
Guided learning
0h
Autonomous learning
30h

Teaching methodology

On-site Activities:
- Lectures: Two hours per week (whole group).
- Problem-Solving and visualization of molecules: Two hours per week (the theory group is divided into two subgroups).

Evaluation methodology

For the evaluation of the subject, the grade of the partial exam (P), the grade of the final exam (F) and the grade of tasks during the course (T) will be taken into account and will
be combined with the following formula:
Grade=max(0.25*P+0.1*T+0.65*F)

A student is considered to have taken the subject if they take the final exam. If the student has taken the subject but has failed, then the student may take the re-
evaluation exam (RT) and in this case the grade for the subject will be 1*RT (the partial score is not used).

Bibliography

Basic:

Complementary:

Previous capacities

Basic concepts of chemistry, be familiarised with the basic principles governing chemical reactions, including stoichiometry (quantitative relationships in chemical reactions), chemical elements and compounds.