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Fundamentals of Chemistry and Biophysics
| Code: | M113 | Acronym: | FQB |
| Keywords | |
|---|---|
| Classification | Keyword |
| OFICIAL | Medicine |
Instance: 2021/2022 - 1S (of 04-10-2021 to 14-01-2022) 
| Active? | Yes |
| Responsible unit: | Chemistry |
| Course/CS Responsible: | Integrated Masters Degree in Medicine |
Cycles of Study/Courses
| Acronym | No. of Students | Study Plan | Curricular Years | Credits UCN | Credits ECTS | Contact hours | Total Time |
|---|---|---|---|---|---|---|---|
| MIM | 188 | Official Study Plan | 1 | - | 6 | 56 | 162 |
Teaching language
PortugueseObjectives
1. Generally, to explain how biological molecular components, and its supramolecular organizations, work, and can be studied, based on some of the most fundamental models of Physics and of Chemistry.2. To apply Physics models to the description of some instrumental methods of diagnostic and therapeutic, as well as to how the results from said methods may be medically used.
3. To apply Chemistry models to the description of the most important structural and reactional properties of biological carbon compounds.
4. To systematize specific knowledge about the structure of the most important biological molecules as well as how that structure relates to the biological "function".
Learning outcomes and competences
1. To understand and use basic principles of Physics that are relevant to the life sciences and specifically to the acquisition of medical data, like, for example, medical image.
2. Knowledge of the biologically important carbon compounds reactions and their mechanisms. Basic organic chemistry problem solving.
3. Structural knowledge of the most important types of biological molecules.
4. Understanding of the importance of molecular recognition, intermolecular interaction and the hydrophobic effect in biological chemistry.
5. Ability to explain the function and action mechanism of biological compounds based on its molecular structure and reactivity, namely enzymes' catalysis, kinetics and regulation.
6. Understanding of the main metabolism global organization, namely the integration of anabolism and catabolism made by NAD (and FAD) and ATP (and other NTPs).
Working method
PresencialProgram
THEORETICAL PROGRAM
A - Image / Diagnosis
1. Radioactivity and radiation. Biological effects. Biological applications (structural biophysics, diagnosis / imaging). Radioisotopes used in medical imaging.
2. Magnetism. Magnetic resonance imaging. Biological applications (diagnosis and imaging). Contrast agents.
3. Ultrasounds. Doppler effect. Image. Contrast agents.
B - Organic Chemistry
1. Alkanes: Classification of alkanes. Hybridization sp3. Sigma connection. Structures of methanes and other linear, branched and cycloalkanes. Physical properties of alkanes and cycloalkanes. Conformation and conformational analysis of ethane and butane. Conformation of cycloalkanes. Substituted cyclohexanes - axial and equatorial hydrogens.
2. Alkenes and alkynes: Sp2 hybridization. Pi bond. Nomenclature of alkenes - the system E and Z. Nomenclature of alkynes. Physical properties of alkenes and alkynes. Hydrogen deficiency index. Relative stability of alkenes. alkynes: hybridization sp.
3. Stereochemistry: Isomerism: Constitutional isomerism and stereoisomers. Enantiomers and diastereoisomers. Enantiomers and chiral molecules. Elements of symmetry. Nomenclature of enantiomers: the R and S system. Properties of enantiomers. Optical activity. Polarimeter. Specific rotation. The origin of optical activity. Racemic form. Enantiomeric purity, optical purity and enantiomeric excess. Molecules with more than one stereocenter. Meso compounds.
4. Aromatic Compounds: Kekule Structure for Benzene. Molecular orbital of benzene. Polycyclic aromatic hydrocarbons. Heterocyclic aromatic compounds. Aromatic compounds in biochemistry. Mechanism of oxidation-reduction by NAD+ and NADH.
5. Alcohols, Phenols, Thiols and Amines: Structure and nomenclature of alcohols and ethers. Physical properties of alcohols and ethers. Hydrogen bonds of alcohol. Nomenclature of phenols. Physical properties of phenols. Thiols, thioethers and thiophenols. Tissue disulfides in biochemistry. Classification and nomenclature of amines. Heterocyclic amines Basicity of amines. Biologically important amines.
6. Aldehydes and Ketones: Compounds with carbonyl group. Types of carbonyl compounds. Molecular orbital of the carbonyl group. Physical properties of aldehydes and ketones. Nomenclature of aldehydes and ketones. Photochemistry of vision.
7. Carboxylic Acids: Carboxylic Acid Derivatives. Carboxylic acid nomenclature. Physical properties of carboxylic acid. Acidity of carboxylic acids. Ester synthesis: Esterification. Base catalyzed ester hydrolysis: Saponification. Lactones: formation and hydrolysis. Amides and lactams. Beta lactam antibiotics-penicillins and cephalosporins. Resistance to penicillins.
C - Biomolecules: structure and function
1. Water: Water as a biological solvent, hydrophobic effect. Water as a biological reagent.
2. Carbohydrates. Definitions of carbohydrates. Classification of monosaccharides-aldose and ketosis. Designation D and L of monosaccharides. Structural formulations for monosaccharides. D - (+) - glucose anomers. Mutarotation and formation of glycoside. Dissaccharides: sucrose. Invert sugar. α- and β-Maltose: 1,4-α-Glucoside linkage. α- and β-cellobiose: 1, 4-β-glucosidic linkage. Polysaccharides. Starch-amylose and amylopectin. Glycogen and cellulose. Deoxy sugars-2-Deoxyribose. Sugars containing nitrogen-glycosylamines, amino sugars. Chitin and chitosan. Carbohydrates on cell surfaces.
3. Amino acids and proteins: Amino acids. Energetics of the biological synthesis of the peptide bond. Proteins, Secondary structure, Disulfide bridges between cysteine residues, Tertiary structure. Factors that interfere with protein conformation. Graphical representation of proteins and their interpretation. Quaternary Structure. Main types of biological proteins and their functions. Molecular recognition, induced complementarity. Examples of structural proteins, Examples of hormonal peptides. Examples of immunoglobulins.
4. Enzymes: Chemical kinetics. Definition of average and instantaneous rate of chemical reactions. Distinction between rate and extension (equilibrium constant) of reaction. Elementary and non-elementary reactions. Rate equations and displacement equations. Simple models of pharmacokinetics. Catalysis in homogeneous medium, enzymatic catalysis. Complex enzyme-substrate, Transient state energetics. Examples of enzymatic mechanisms. Michaelis-Menten chemical model (MM). Kinetic equation of MM, Definition of maximum rate, Interpretation of the equation and its linearization, Interpretation of constants k2, Km and k2 / Km, Examples of kinetic constants for various enzymes. Molecular recognition in the context of enzymes.
A - Image / Diagnosis
1. Radioactivity and radiation. Biological effects. Biological applications (structural biophysics, diagnosis / imaging). Radioisotopes used in medical imaging.
2. Magnetism. Magnetic resonance imaging. Biological applications (diagnosis and imaging). Contrast agents.
3. Ultrasounds. Doppler effect. Image. Contrast agents.
B - Organic Chemistry
1. Alkanes: Classification of alkanes. Hybridization sp3. Sigma connection. Structures of methanes and other linear, branched and cycloalkanes. Physical properties of alkanes and cycloalkanes. Conformation and conformational analysis of ethane and butane. Conformation of cycloalkanes. Substituted cyclohexanes - axial and equatorial hydrogens.
2. Alkenes and alkynes: Sp2 hybridization. Pi bond. Nomenclature of alkenes - the system E and Z. Nomenclature of alkynes. Physical properties of alkenes and alkynes. Hydrogen deficiency index. Relative stability of alkenes. alkynes: hybridization sp.
3. Stereochemistry: Isomerism: Constitutional isomerism and stereoisomers. Enantiomers and diastereoisomers. Enantiomers and chiral molecules. Elements of symmetry. Nomenclature of enantiomers: the R and S system. Properties of enantiomers. Optical activity. Polarimeter. Specific rotation. The origin of optical activity. Racemic form. Enantiomeric purity, optical purity and enantiomeric excess. Molecules with more than one stereocenter. Meso compounds.
4. Aromatic Compounds: Kekule Structure for Benzene. Molecular orbital of benzene. Polycyclic aromatic hydrocarbons. Heterocyclic aromatic compounds. Aromatic compounds in biochemistry. Mechanism of oxidation-reduction by NAD+ and NADH.
5. Alcohols, Phenols, Thiols and Amines: Structure and nomenclature of alcohols and ethers. Physical properties of alcohols and ethers. Hydrogen bonds of alcohol. Nomenclature of phenols. Physical properties of phenols. Thiols, thioethers and thiophenols. Tissue disulfides in biochemistry. Classification and nomenclature of amines. Heterocyclic amines Basicity of amines. Biologically important amines.
6. Aldehydes and Ketones: Compounds with carbonyl group. Types of carbonyl compounds. Molecular orbital of the carbonyl group. Physical properties of aldehydes and ketones. Nomenclature of aldehydes and ketones. Photochemistry of vision.
7. Carboxylic Acids: Carboxylic Acid Derivatives. Carboxylic acid nomenclature. Physical properties of carboxylic acid. Acidity of carboxylic acids. Ester synthesis: Esterification. Base catalyzed ester hydrolysis: Saponification. Lactones: formation and hydrolysis. Amides and lactams. Beta lactam antibiotics-penicillins and cephalosporins. Resistance to penicillins.
C - Biomolecules: structure and function
1. Water: Water as a biological solvent, hydrophobic effect. Water as a biological reagent.
2. Carbohydrates. Definitions of carbohydrates. Classification of monosaccharides-aldose and ketosis. Designation D and L of monosaccharides. Structural formulations for monosaccharides. D - (+) - glucose anomers. Mutarotation and formation of glycoside. Dissaccharides: sucrose. Invert sugar. α- and β-Maltose: 1,4-α-Glucoside linkage. α- and β-cellobiose: 1, 4-β-glucosidic linkage. Polysaccharides. Starch-amylose and amylopectin. Glycogen and cellulose. Deoxy sugars-2-Deoxyribose. Sugars containing nitrogen-glycosylamines, amino sugars. Chitin and chitosan. Carbohydrates on cell surfaces.
3. Amino acids and proteins: Amino acids. Energetics of the biological synthesis of the peptide bond. Proteins, Secondary structure, Disulfide bridges between cysteine residues, Tertiary structure. Factors that interfere with protein conformation. Graphical representation of proteins and their interpretation. Quaternary Structure. Main types of biological proteins and their functions. Molecular recognition, induced complementarity. Examples of structural proteins, Examples of hormonal peptides. Examples of immunoglobulins.
4. Enzymes: Chemical kinetics. Definition of average and instantaneous rate of chemical reactions. Distinction between rate and extension (equilibrium constant) of reaction. Elementary and non-elementary reactions. Rate equations and displacement equations. Simple models of pharmacokinetics. Catalysis in homogeneous medium, enzymatic catalysis. Complex enzyme-substrate, Transient state energetics. Examples of enzymatic mechanisms. Michaelis-Menten chemical model (MM). Kinetic equation of MM, Definition of maximum rate, Interpretation of the equation and its linearization, Interpretation of constants k2, Km and k2 / Km, Examples of kinetic constants for various enzymes. Molecular recognition in the context of enzymes.
5. Nucleic acids: ribonucleotides and deoxyribonucleotides, phosphodiester bond formation reaction. Watson-Crick bonding by hydrogen bridges between nucleotide bases, stacking of bases in water. DNA, DNA replication, RNA, Aminoacyl-tRNA synthetases, Definition of the genetic code. Ribosome, conjugated function of rRNA, mRNA and tRNA.
6. Bioenergetics: Redox cycles in the biosphere, steady state. States of carbon oxidation. Hydrolysis of ATP, ATP in the synthesis of biological bonds via nucleophilic substitution.
LABORATORY PROGRAM
1. Laboratory Techniques
2. Identification of carbohydrates
3. Determination of total serum cholesterol
4. DNA denaturation and spectrophotometry
5. Invertase kinetics
Mandatory literature
Joseph W. Kane ; PhysicsT.W. GRAHAM SOLOMONS and CRAIG B. FRYHLE; Organic Chemistry, 10th Edition, John Wiley & Son, Inc, 2011
José Augusto Pereira; Apontamentos de Química Biológica, ICBAS, 2014 (Freely available as eBook (PDF) in "Documents" page (FQB page, this site))
Comments from the literature
T.W. GRAHAM SOLOMONS and CRAIG B. FRYHLE; Organic Chemistry, 10th Edition, John Wiley & Son, Inc, 2011José Augusto Pereira; Apontamentos de Química Biológica, ICBAS, 2014 (Freely available as eBook (PDF) in "Documents" page (FQB page, this site)
Teaching methods and learning activities
Theoretical classes, presential or online, using Powerpoint presentations. Theoretical-practical classes, presential or online, of problem solving and matters related with laboratorial works. Laboratorial classes where the students work in groups of up to 3, following a written protocol.Evaluation Type
Distributed evaluation with final examAssessment Components
| Designation | Weight (%) |
|---|---|
| Exame | 100,00 |
| Total: | 100,00 |
Amount of time allocated to each course unit
| Designation | Time (hours) |
|---|---|
| Estudo autónomo | 106,00 |
| Frequência das aulas | 56,00 |
| Total: | 162,00 |
Eligibility for exams
Presence in at least 75% of the whole practical and laboratorial classes.Calculation formula of final grade
Naming of evaluation tests (20 points each): A1 (1st partial), A2 (2nd partial), EN (1st global), ER (2nd global)
Options to get course approval, N >= 9.50 points:
(1) N = 0,5 x A1 + 0,5 x A2
(2) N = EN
(3) N = ER
Tests A2 and EN are simultaneous and therefore mutually exclusive. It is possible to change from option (1) to options (2) or (3) but that entails to discard the grade obtained on A1 permanently.
Observations
Students are not allowed to enter the classes 10 minutes after its beggining time. Adequate lab coats are mandatory in laboratorial classes.
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