Biological and Organic Chemistry

Code:

EBE0009

Acronym:

QOBI

Keywords
Classification	Keyword
OFICIAL	Basic Sciences

Instance: 2018/2019 - 2S

Active?	Yes
Web Page:	https://moodle.up.pt/course/view.php?id=2112
Responsible unit:	Chemistry
Course/CS Responsible:	Master in Bioengineering

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
MIB	100	Syllabus	1	-	6	70	162

Teaching language

Portuguese

Objectives

Carbon compounds are the chemical building blocks of life either through simple molecules or more complex ones, examples of which are amino acids or carbohydrates and the respective polymers, among many others. Thus, the main objective of this course is for students to develop the ability to recognize, understand and integrate the principles and rules governing the structures, interactions and chemical transformations of organic molecules and their application to the understanding of the structure of biological molecules and how the structure and properties of these molecules contributes to the construction, development and function of living systems.

Learning outcomes and competences

Working method

Presencial

Pre-requirements (prior knowledge) and co-requirements (common knowledge)

It is deemed advisable basic knowledge in general chemistry, including atomic and molecular structure, chemical bonding, chemical kinetics, acid-base properties and thermodynamics.

Program

Atomic and Molecular Structure - The chemical Bond. Molecular Geometry. Valence Shell Electron Pair Repulsion Theory (VSEPR). Valence Bond Theory (VBT). Hybridization of atomic orbitals. Molecular Orbital Theory (MOT). Bonding and antibonding molecular orbitals. Delocalized chemical bond.

IUPAC Rules for Naming Organic Compounds: Linear, Cyclic and Aromatic. Alkanes, Alkenes and alkynes. Main group. Choose and numbering of the fundamental structure. Alcohols, thiols, ethers, sulphides, phenols,  halides, amines, aldehydes, ketones, carboxylic acids, amides, esters, acyl halides, salts, thioesters.

Stereochemistry – Definition of Isomerism and stereoisomerism. Biological examples. Brief historical perspective. Chirality and its biological importance. Enantiomers and Diastereoisomers. Newmann, Fischer, Wedge-and-Dash representations. Absolute Configuration: the R/S system. Optical activity. Biological examples. Racemic mixture. Meso compounds. The D and L System in carbohydrates and amino acids. Chirality without stereogenic centers. Prochirality. Biological examples. Geometric isomerism: Cis/trans and E/Z isomers. Biological examples. Conformational analysis: Staggered and eclipsed conformations in alicyclic and cyclic compounds. Biological examples. Stereoisomery in cyclic compounds. Biological examples.

Structure and Reactivity – Reactivity: kinetic and thermodynamic principles. Potential energy diagram. Cleavage of chemical bonds and enthalpy change. Theory of collisions. Free Energy Variation. Intermediaries and transition states. Maxwell-Boltzmann distribution curves. Electronic availability. Inductive and mesomeric effects and their influence in reactivity. Dipolar moment. Biological examples. Acidity and basicity of organic compounds: inductive, mesomeric and size effects. Stability and reactivity of phosphoanhydride bond: ATP, phosphoenolpyruvate, 1,3-bisphosphoglycerate. Reaction Mechanism. Type of reactions. Homolytic and heterolytic reactions and their Intermediates: nucleophiles, electrophiles and free radicals. Examples of biological and non-biological homolytic processes.

Saturated and Insaturated hydrocarbons. Alkanes and alkenes: physical properties. Structure, bond type and bond energy in alkenes. Representative biological examples. Catalytic hydrogenation. Biological example. Relative stability. Electrophilic addition to alkenes: general mechanism. Energy Diagram. Electrophilic addition of hydrogen halides to alkenes. Markovnikov rule. Carbocation stability: hyperconjugation and resonance. Hydration of alkenes. Biological example. Addition to conjugated dienes. Addition of halogens. Halohydrins formation. Reaction with peroxyacids. Epoxides hydration. Some biological examples.Formation of glycols. 

Aromatics and heteroaromatics compounds – Biological examples of aromatic compounds. Allotropic forms of carbon atom. Aromaticity. Benzene, polycyclic and heteroaromatic compounds. Hückel rule. Physical proprieties. Resonance energy. Biological relevance. Electrophilic aromatic substitution: Nitration, halogenation, Friedel-Crafts alkylation and acylation. Activating and deactivating groups. Substitution orientation. Biological examples.

Nucleophilic aliphatic substitution (S_N)  and elimination reactions (E) - Biological examples of S_N reactions. Mechanisms of SN reactions: S_N1 and S_N2. S_N2: general mechanism, kinetics, stereochemistry, inversion of configuration and biological example. S_N1: general mechanism, kinetics, stereochemistry and biological example. Alkyl halides: physical properties and chemical reactivity. Relative reactivity, S_N1 vs S_N2: effect of solvent, structure, substrate, nucleofile and leaving group in reactivity. Biological examples of Elimination reactions. Elimination reactions: mechanism of E1 and E2 - general mechanism, kinetics, stereochemistry and biological example. E1 vs E2. Elimination vs substitution. 

Aldehydes and ketones – Functional groups containing the carbonyl group. Physical proprieties and characteristic reactions of carbonyl group. Examples of biological compounds with the aldehyde or ketone group. State of oxidation of organic molecules. Aldehydes and ketones reduction: hydride addition. Biological examples. Nucleofilic addition reactions: acidic and basic catalysis. Addition of water. Addition of alcohols:Hemiacetals and acetals. Biological examples. Reactions with amines: imines and enamines. Biological examples. Alfa hydrogen acidity. Keto-enolic tautomerism. Biological examples. Carbonyl compounds condensation reactions. Biological examples.

Carbohydrates – General information on carbohydrates. Examples. Classification and denomination. Optical activity. Structural representation. Cyclic structures of monosaccharide’s and their anomeric forms. Reducing sugars. Mutarotation. Monosaccharide’s conformation.  Monosaccharide derivatives. Glucosides. Glucose binding: synthesis and chemical and enzymatic hydrolysis. Oligo- and polysaccharides. Example of biosynthesis of the glycosidic linkage. Structure and backup polysaccharides: starch, glycogen, dextrans, cellulose, chitin, agar, agarose, agaropectins, peptidoglycan, biofilms. Other important carbohydrates: amino sugars, proteoglycans, glycoproteins, mucins and lipopolysaccharides.

Carboxylic acids and derivatives - Structure and physical properties. Biological Examples. Effects of substituents on acidity. Preparation of carboxylic acids: biological examples. Reduction of carboxylic acids. Nucleophilic substitution reactions and derivatising: preparation of esters, transesterification, formation of amides. Formation of Lactonas: biological example. Formation of proteins. Relative reactivity of carboxylic acid derivatives. Ester hydrolysis. Biological examples. Claisen condensation reaction. Biological example.

Lipids - Definitions and classifications of lipids. Physical properties. Main biological functions. Fatty Acids - biological structure, properties, reactivity and functions. Essential fatty acids. Acylglycerides. Catalytic hydrogenation. Saponification. Waxes. Phosphoglycerides. Sphingolipids: phospho-sphingolipids and glucosphingolipids. Cerebrosides and gangliosides. Icosanoides. Terpenoids. Example of biosynthesis. Steroids: general structure and functions. Plasma lipoproteins: structure and function.

Amines and amides - Type of amines: 1st, 2nd and 3rd, aliphatic, aromatic and heteroaromatic. Biological examples of amines. Structure and physicochemical properties of amines. Effect of substituents on basicity.  Amides: physicochemical properties, synthesis and hydrolysis. Biological example. Polymers of amides. Biological examples. Biological example of the enzymatic hydrolysis reaction mechanism of proteins

Amino acids, Peptides and Proteins - Overview of peptides and proteins. Amino acids structures and their classification. Amino acid features: dimension, charge, polarity, hydrophobicity, stereochemistry. Essential and unusual amino acids. Characteristics of the peptide bond and three-dimensional implications. Peptides and proteins - features and levels of organization: the primary, secondary, tertiary and quaternary structures of proteins; Motifs and Domains. Alfa helix and beta plated sheet. Turns. Graphics by Ramachandran. Stabilization and denaturation forces. Functions of peptides and proteins. Example of hormonal peptides, immunoglobulins, MHC. Fibrous proteins: alpha-keratin, fibroin, collagen. Toxins and Venoms. Non-ribosomal peptides. Endogenous opiates.

Laboratory classes: 

- Ultraviolet-Visible spectrophotometry – General principles of the Instrumental Method. Beer-Lambert Law. Factors affecting the absorption of UV-Vis radiation. Linearity and Deviations from linearity. Instrumentation. Calibration Curve. Applications Examples (TP class).

- Extraction, Identification and Purification of Caffeine from Black Tea Leaves.

-  Determination of reducing sugars by DNS method.

- Kinetic Control vs. Thermodynamic Control of a reaction.

Mandatory literature

Solomons T. W. Graham; Organic chemistry. ISBN: 978-0-470-52459-6
Morrison Robert T.; Química orgânica
Nelson David L.; Lehninger principles of biochemistry. ISBN: 1-57259-931-6
Quintas Alexandre 340; Bioquímica. ISBN: 978-972-757-431-5

Complementary Bibliography

Vollhardt K. Peter C.; Organic chemistry. ISBN: 978-1-4292-3924-0
Berg Jeremy M.; Biochemistry. ISBN: 978-1-4292-7635-1

Teaching methods and learning activities

At the beginning of the semester students are introduced to the program,scheduled for classes and interim evaluation.

In TP classes the formal presentation of the study subjects is made via projection of slides in Power Point using computer and video projector. These slides are previously available to students. For different chapter worksheets with exercises are provided. All this material is available through the e-learning platform.Students are encouraged to participate with questions or comments during class.

Several laboratory classes are performed so that students have contact not only with the basic laboratory techniques of organic chemistry, but also to apply and consolidate the acquired theoretical concepts with the practical application.

Software

Chemsketch 2015

keywords

Physical sciences > Chemistry > Organic chemistry
Physical sciences > Chemistry > Biochemistry

Evaluation Type

Distributed evaluation with final exam

Assessment Components

Designation	Weight (%)
Exame	80,00
Trabalho laboratorial	20,00
Total:	100,00

Amount of time allocated to each course unit

Designation	Time (hours)
Estudo autónomo	92,00
Frequência das aulas	42,00
Trabalho laboratorial	28,00
Total:	162,00

Eligibility for exams

According with the current regulations. 
Are exempted from verification of attendance all cases provided by law and that students which, in the previous school year, have satisfied the attendance and have obtained a classification of the laboratory equal to or greater than 9.5.

Calculation formula of final grade

Students can choose to be evaluated only in a final examination or through an alternative evaluation scheme with two partial tests (A1 and A2). 

The final grade is the final exam, where students choose to be evaluated only through that exam.

In the alternative evaluation scheme, students can conduct a partial evaluation test, which classification is called A1. Continuing to follow this scheme, students perform in Regular Season Testing a second evaluation test, whose classification is called the A2, which together with the examination A1 becomes equivalent to the exam realized in Normal Period, with no minimum score on the shares. The final grade of the UC will be calculated accordingly: (0.8 x Exam) + (0.2 x Practice) or [0.8 x (A1 + A2) / 2] + (0.2 x Practice). A minimum of 9.5 in the average evaluation components A1 and A2 or exams is required to be approved.

 

Examinations or Special Assignments

There are not planned special jobs.

Special assessment (TE, DA, ...)

According with the current regulations.

Classification improvement

According with the current regulations.