Topic 2.pptx

BIOL1201 Introduction to Biochemistry Shareen J. Arnold O’Sullivan MSc.; MEng. 2022-1 Objectives (week 2) Chapter 10.2-10.3, 11.1-11.4 [Denniston 7th Edition] Introduction to Biochemistry •Hydrocarbons: intro to alkanes, alkenes, & alkynes •Nomenclature/drawings aliphatic and alicyclic alkanes, a...

BIOL1201 Introduction to Biochemistry Shareen J. Arnold O’Sullivan MSc.; MEng. 2022-1 Objectives (week 2) Chapter 10.2-10.3, 11.1-11.4 [Denniston 7th Edition] Introduction to Biochemistry •Hydrocarbons: intro to alkanes, alkenes, & alkynes •Nomenclature/drawings aliphatic and alicyclic alkanes, alkenes, & alkynes •Functional groups in organic compounds •Biomolecules Alkanes nomenclature Rules for naming alkanes (unbranched): *suffix – “ane” *General formula: C H n # of C’s prefix metha etha *1st ten members: propa buta penta hexa hepta octa nona deca IUPAC name formula +2 2n alkane structure *structural formula Alkanes nomenclature Rules for naming alkanes *alkyl groups – branches on the C chain (branched): *have one less H than simple alkanes *suffix – “yl” Alkanes nomenclature How to identify the parent chain from the substituent???? How to give lowest possible locant to substituents???? Alkanes nomenclature 1) Find longest continuous chain (parent chain) 2) Identify substituents (branches) decan e Alkanes nomenclature 3) Give lowest locant to substituents when numbering your parent chain Alkanes nomenclature 4) Other rules:Substituents: *names are written in front of the parent name in an alphabetical order *are assigned prefixes if there is more than one of the same kind [2 - di, 3 – tri, 4 – tetra, 5 – penta, 6 – hexa, 7 – hepta, 8 – octa, 9 – nona, 10 – deca] *conventionally, halogens substituents are named before alkyl group substituents; but alphabetical order is priority Alkanes nomenclature 4) Other rules:Numbers: *are separated by commas from other numbers *are separated from names by hypen Alkanes nomenclature Alkanes nomenclature Examples of names of branched alkanes Example 1: Alkanes nomenclature Examples of names of branched alkanes Example 2: Practice problems Give the IUPAC names for the following molecules: Practice problems Give the IUPAC names for the following molecules: 2,2-dimethylpropane 3,3,5-trimethylheptane 3-ethyl-3-methylhexane 2,4-dimethylhexane 2,3,3-trimethylpentane 2,2,4-trimethylpentane heptane 3,3-dimethylpentane 3,3-diethyl-2,2,4-trimethylhexane 3,5-dimethyl-5-propyloctane Alkanes nomenclature When to use iso? Iso = “isomer of” *iso means attachment at the second carbon *common name system butane octane isobutane (2-methylpropane) isoctane (2,2,4-trimethylpentane) Alkanes nomenclature draw the structure of 4-tert-butyl-4-methyloctane 4 butyl 4 groups: 1 3 2 1 1 3 2 2 3 4 4 3 2 4 1 tertbutyl Alkyl Halide nomenclature Rules for naming halogen/alkyl halide): 2-chloro-2- 2-chloro-2,3- 1-chloro2,2- Alkanes nomenclature Comparing alkanes with cycloalkanes: condensed molecular skeletal molecular Alkanes nomenclature Rules for naming cycloalkanes: 1) same naming rules apply; except now prefix “cyclo-” is used 2) One substituent requires no numbering methylcyclohexane tert-butylcyclopentane Alkanes nomenclature Rules for naming cycloalkanes: 3) more than one substituent – assign # with the lowest locant 4) different substituents – assign lower # to substituents alphabetically 1,3-dimethylcyclohexane 1-ethyl-3-methylcyclohexane Alkenes nomenclature Rules for naming alkenes (unbranched): *suffix – “ene” *General formula: C H n # of C’s formula IUPAC name ethene 2n Alkene structure ethene (smallest member) propene *1st nine members: but-1-ene pent-1-ene propene “positional isomers” hex-1-ene but-1-ene hept-1-ene oct-1-ene or 1-butene non-1ene pent-1-ene dec-1-ene or 1-pentene The rules for naming alkenes is similar to that of alkanes; except the ending is “-ene” and the double bond is given the lowest locant and determines the locant of the substituents. hex-1-ene or 1-hexene hex-2-ene or 2-hexene but-2-ene or 2-butene pent-2-ene or 2-pentene hex-3-ene or 3-hexene Examples of condensed formulas of alkenes Examples of branched alkenes 3 2 ethene propene 4 1 2-chloro-2-butene or 2-chlorobut-2-ene butene pentene 5 6 hexene 4 3 2 1 2,3,3,4,4,5-hexamethyl-1-hexene or 2,3,3,4,4,5-hexamethylhex-1-ene Alkenes nomenclature *Examples of simple cycloalkenes cycloalkane cyclopropane cyclobutane cyclopentane cyclohexane cycloalkene cyclopropene cyclobutene cyclopentene cyclohexene Alkenes nomenclature *Location of the = is between 1 and 2 always 1 5 2 1 1 2 3 3 6 1 4 6 3 2 1 2 3 3-methylcycloheptene 1-methylcyclopentene a) Draw 1-methyl-4-tert-butylcyclohexene. b) Name the following compound. 5 2 3 4 1,6-dimethylcyclohexene Alkenes nomenclature Answers: a) Draw 1-methyl-4-tert-butylcyclohexene. b) Name the following compound. 2,6-dimethyl-2,5-heptadiene Alkynes nomenclature Rules for naming alkynes (unbranched): *suffix – “yne” *General formula: C H n ethyne n Alkyne members also possess “positional isomers” e.g. 1-pentyne and 2-pentyne *1st five members: propyne butyne Examples of branched alkynes pentyne hexyne 4-methyl-2-heptyne Alkynes nomenclature *same rules of nomenclature as alkenes; except the ending is –”yne” 6-methyl-3-octyne (new: 6-methyloct-3-yne) ethyne 3,3-dimethyl-1-butyne 2-butyne 4-bromo- 2-hexyne 3-methylcyclononyne 2,5-dimethyl-3-hexyne Alkynes nomenclature *Examples to practice with: Functional groups Group carbon-carbon single bond Structural formula Family Family alkane carboxylic acid carbon-carbon double bond alkene 1° carbon-carbon triple bond alkyne or thiol benzene ring aromatic ether or alkoxy group ether ester bond or linkage ester (acid + alcohol) Peptide bond amide Halogen atom amine Alkyl halide or haloalkane thiols phosphate An atom or group of atoms that undergoes a reaction/gives rise to physical/chemical properties of a molecule. Practice polyfunctional compounds Practice hydrox yl benzen e ring amino group alkoxy/ ether benzen e ring double bond carbon yl polyfunctional compounds benzen e ring peptid e chloro tripl e bond est er Carbox yl carbon yl Functional groups Functional groups Functional groups Functional groups Functional groups Functional groups Functional groups Organic compounds are diverse! • forms chains, branches and rings • contain CHON etc and can be complex carbohydrates proteins lipids nucleic acids POLL A B Complete ACHIEVE 1: Intro to Biochemistry END