chem1004-exam-notes.pdf - CHEM1004 EXAM NOTES TOPIC 1 – FUNDAMENTALS OF BIOLOGICAL CHEMISTRY Early theories of vitalism were refuted by development of

chem1004-exam-notes.pdf - CHEM1004 EXAM NOTES TOPIC 1 –...

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CHEM1004 EXAM NOTES TOPIC 1 – FUNDAMENTALS OF BIOLOGICAL CHEMISTRY Early theories of vitalism were refuted by development of synthesis or organic compounds such as urea or acetic acid from non-organic molecules Organic compounds are carbon-based structures; carbon is suited for the role as the backbone of organic molecules due to its bonding capacity and structural variations of carbon bonding modes (tetrahedral, linear, trigonal) Organic compounds are based on carbon and hydrogen, but may contain other heteroatoms (O, N, S, P, Cl) Covalent bonds are bonds in which electrons are shared between two atoms. Some atoms differ in their electronegativity (tendency to attract electron) When atoms with different electronegativity form covalent bonds, the electrons tend more towards the more electronegative atom, resulting in a polar bond The more electronegative atom attracts more electrons and is given a partial negative charge ( δ - ) ; the less electronegative atom attracts less electrons and is given a partial positive charge ( δ + ). A formal charge arises when an atom has more or less valence electrons or covalent bonds than required for a neutral charge A reactive intermediate is a transient, short-lived molecule in the transition state of one molecule to another; reactive intermediate of carbon include carbanions, carbocations, radicals, carbenes etc. Intramolecular forces of organic molecules are usually covalent bonds and function to hold the molecule together; intramolecular forces influence the chemical properties of the molecule Intermolecular forces occur between molecules and influence the physical properties of the molecule (melting point, boiling point) and are mostly non- covalent bonds including dispersion forces, dipole interactions, hydrogen bonds and ionic bonds Functional groups in organic chemicals often give the molecule certain properties, and help in classification of the molecule
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The chemical structure and the arrangement of atoms in 3D space of a chemical determines the physical, chemical and biological properties Stereoisomers are compounds that have the same chemical formula but differ in their spatial arrangement Cis/trans isomers occur due to carbon-carbon double bonds (alkene) that don’t allow rotation around the bond Benzene is an interesting molecule in which the electron orbitals are delocalised over the entire ring structure (resonance) ; the property of resonance makes a stable aromatic compound such as benzene Many aromatic compounds are heterocycles that contain heteroatoms (e.g. nitrogen) Functional groups that commonly occur in nature include: Alkenes are carbon-carbon double bonds that; comprise of one sigma bond (low-energy axial bonds) and one pi bond (higher- energy bonds that occur as lobes above or below the sigma bond) Alkynes are carbon-carbon triple bonds that consist of one sigma bond and two pi bonds (one above and one below) Alcohol
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