Biological and Organic Chemistry

Code:

EBE0009

Acronym:

QOBI

Keywords
Classification	Keyword
OFICIAL	Basic Sciences

Instance: 2012/2013 - 2S

Active?	Yes
Web Page:	https://moodle.fe.up.pt/1213/course/view.php?id=394
E-learning page:	https://moodle.fe.up.pt/
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	105	Syllabus	1	-	5	42	135

Teaching language

Portuguese

Working method

Presencial

Program

Atomic and Molecular Structure - The Chemical Bond. Molecular Geometry. Valence Shell Electron Pair Repulsion Theory (VSEPR). Valence Bond Theory. Hybridiztion of Atomic Orbitals. Molecular Orbital Theory. Bonding and Antibonding Molecular Orbitals. Delocalized Chemical Bond

Stereochemistry – Isomers and stereoisomers. Chirality. Enantiomers and diastereoisomers. Newmann, Fischer, Wedge-and-Dash representations. Absolute Coniguration: the R/ system. Meso compounds. The D and L System. Chirality without stereogenic centers. Prochirality. Cis/trans and E/Z isomers. Conformational analysis. Staggered and eclipsed conformations. Stereoisomery in ciclic compounds. Optical activity. Racemic mixture.

Structure and Reactivity – Indutif and mesomeric effects and their influence in reactivity. Nucleophiles and electrophiles. Kind of reactions. Arrhenius Collision theory. Homolitic and heterolitic reactions and their intermediates. Some examples of homolitic processes.

Saturated and Insaturated hydrocarbons. Alkanes and alkenes: physical proprieties. Structure, bond type and bond energy in alkenes. Electrophilic addition: general mechanism. Electrophilic addition of hydrogen halides to alkenes. Markovnikov rule. Carbocation stability. Hydration of alkenes. Addition to conjugated dienes. Addition of halogens. Reaction with peroxyacids. Epoxides hidration. Some biological examples.

Aromatics and heteroaromatics compounds – Aromaticity. Hückel rule. Physical proprieties. Resonance energy. Heteroaromatic compounds and their biological significant. Electrophilic aromatic substitution: Nitration, halogenation, Friedel-Crafts alkylation and acylation. Biological examples.

Alkyl halides - Nucleophilic substitution reactions. SN2 and SN1 type reactions: mechanisms, kinetics and stereochemistry. SN1 vs SN2: effect of solvent, structure and leaving group in reactivity. Elimination reactions: mechanism of E1 and E2 reactions. E1 vs E2. Elimination vs substitution.

Aldehydes and ketones – Physical characteristics of carbonyl group. Physical proprieties and characteristic reactions. Alfa hydrogen acidity. Keto-enolic tautomerism. Aldehydes and ketones redution. Oxidation of aldehydes. Carbonyl compounds condensation reactions. Reactions with amines. Biological examples.

Carbohydrates – Classification. Optical activity. Cycic structures of monosaccharides and their anomeric forms. Mutarotation. Monosaccharides conformation. Oxidation of carbohydrates. Oligo- and polysaccharides. Glycosidic bond. Some others significant carbohydrates: aminosugars, glico proteins, mucopolyssaccharides.

Carboxylic Acids and derivatives - Physical Structure and properties. Effect of substituent’s on acidity. Reactions of nucleophylic substitution and attainment of derivatives. Relative reactivity of carboxylic acids derivatives.

Lipids - Main biological functions. Fatty Acids - biological structure, properties, reactivity and functions. Neutral Glycerides and Phosphoglycerids. Phospholipids. Sphingolipids. Steroids: general structure and functions. Complex lipids: plasmatic lipoproteins: functions; biological membranes.

Amines - Physical structure and properties. Chemical reactions. Amides and their hydrolysis. Biological example.

Amino acids, Peptides and Proteins - Amino acids structures and their classification. Aminoacid features: dimension, charge, polarity, hidrofobicity. 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. Functions. Denaturation.

Mandatory literature

T. W. Graham Solomons, Craig B. Fryhle ; Organic Chemistry, Danvers, MA : John Wiley & Sons, 2010. ISBN: 978-0-470-52459-6
T. W. Graham Solomons, Craig B. Fryhle; Organic Chemistry. ISBN: 0-471-19095-0
Morrison, Robert T.; Química orgânica
A Quintas, AP Freire, MJ Halpern ; BIOQUÍMICA - Organização Molecular da Vida, lidel, 2008. ISBN: 978-972-757-431-5
Atkins, Robert C.; Organic Chemistry. ISBN: 0-07-009919-7
Stryer, Lubert; Biochemistry. ISBN: 0-7167-2009-4
Nelson, David L.; Lehninger principles of biochemistry. ISBN: 978-0-7167-4339-2

Software

Chemsketch 12.0

Evaluation Type

Evaluation with final exam

Assessment Components

Description	Type	Time (hours)	Weight (%)	End date
Attendance (estimated)	Participação presencial	0,00
	Total:	-	0,00

Eligibility for exams

According with the current regulations.

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.

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 clasification is called the A2, which together with the examination A1 becomes equivalent to the exam realizad in Normal Period. In this case, the final grade is the arithmetic mean of A1 and A2, with no minimum score on the shares.

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.