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BIOL1201 Introduction to Biochemistry Shareen J. Arnold O’Sullivan MSc.; MEng. 2022-1 Objectives (week 1) Chapter 10.1-1-.2 [Denniston 7th Edition] Introduction to Biochemistry •Nature of Carbon -catenation, saturated/unsaturated, aliphatic, alicyclic, aromatic •Orbital hybridization & geometry •...

BIOL1201 Introduction to Biochemistry Shareen J. Arnold O’Sullivan MSc.; MEng. 2022-1 Objectives (week 1) Chapter 10.1-1-.2 [Denniston 7th Edition] Introduction to Biochemistry •Nature of Carbon -catenation, saturated/unsaturated, aliphatic, alicyclic, aromatic •Orbital hybridization & geometry •Organic compound formulas Intro to Biochemistry Chemistry – study of chemicals and their behaviour, properties, reactions Organic Chemistry – study of carbon (C) containing compounds Biochemistry – the chemistry of living things (how biomolecules give rise to chemical processes/life) Nature of Carbon (C) *Over 16 million compounds contain C because of its physical & chemical properties a. covalent bond – share e- b. stable bond – 4 bonds Nature of Carbon (C) c. catenation – form chains one C = different properties *number of C a C is attached to: • • • • primary (1°) – one carbon secondary (2°) – two carbon tertiary (3°) – three carbon quaternary (4°) – four carbon Nature of Carbon (C) d. branches add to diversity of C-containing compounds All are C5H10 Practice question: Label each carbon in each compound as a primary (1°), secondary (2°), tertiary (3°), or quaternary (4°) carbon. Nature of Carbon (C) e. bonds to H,O,N and other elements vanillin chloroform cysteine f. allotrophe – different forms of the same element Nature of Carbon (C) g. saturated and unsaturated compounds double bond single bond (Unsaturat triple ed) bond double bond Nature of Carbon (C) g. saturated and unsaturated compounds Hydrocarbons *the simplest organic compounds containing carbon (C) and hydrogen (H) 3 types: *aliphatic (acyclic) *alicyclic (cyclic) *aromatic Hydrocarbons 1. aliphatic (acyclic) - straight (open) chain or branched • includes 3 families: Alkanes (single), Alkenes (double) & Alkynes (triple) alkan e alkyn e alken e alken e Hydrocarbons 2. alicyclic (cyclic) - ring (closed) chain • includes 3 families: cycloalkanes (single), cycloalkenes (double) & cycloalkynes (triple) cycloalka ne cycloalke ne cycloalky ne Hydrocarbons 3. aromatic (cyclic) - ring of C with alternating single and double bonds. Chemical structure of benzene Bonding in carbon Electrons are in orbitals: A volume of space in which there is a 95% chance of finding an electron governed by 4 quantum numbers: Orbital shapes l=0 1 2 3 4 s p d f g s, p, and d atomic orbitals p (dumbbell shaped) s (spherical) 1s, 2s, and 2p orbitals d (four daisy shaped and one axel shaped) Orbital shapes s p d f ml – maximum # of orbitals for the different values of l *one s orbital *three p orbitals *five d orbitals *seven f orbitals *nine g orbitals Lewis dot structures *shows the valence electrons in an element or compound (bonding and non-bonding e-) Periodic Table (elements 1 – 20) Writing Lewis dot structures *shows the valence electrons in an element or compound (bonding and non-bonding e-) *fill the octet of the central atom Sigma & pi bonds Carbon exhibits covalent bonding (sharing of electrons) Bonds can be classified as: www.difference.wiki/sigma-bond-vs-pibond/ sigma bonds (σ) pi bonds (π) *strongest covalent bond between two atoms *weaker type of covalent bond than σ bond *form when the head of orbitals overlap along the axis *formed by overlapping atomic orbitals *decides the shape of the molecule *decides the length of the molecule *single, double, and triple bonds have 1 σ bond *single bonds have no π bond; double bond has 1 π bond; triple bond has 2 π bonds. The Shape of Molecules/VSEPR Theory VSEPR – Valence Shell Electron Pair Repulsion Theory *bonds have a preferred direction in space *the angles between bonds give a shape *VSEPR explains why different shapes exists: • The # of electron pairs determine the arrangement of electron pairs around the central atom in a molecule • Force of electrostatic repulsion exist between electron pairs. This forces orbitals apart as far as possible • lone pair of electrons have an influence too i.e. # of paired electrons in the valence shell of an atom in a molecule decides the angle between its bond and thus the shape or geometry of the molecules The Shape of Molecules/VSEPR Theory linear trigonal planar tetrahedral C2 H 2 BCl3 CH4 HCN SnCl2 NH3 CO2 C 2H 4 H2 O Based on the molecular formulas above, construct the ball-and-stick model of each molecule. linear ethyne (acetylene) C 2 H2 ball-and-stick model expanded structural *1800 condensed structural *e- are far apart as possible line angel trigonal planar ball-and-stick model boron trichloride BCl3 *1200 expanded structural *3 e- pairs and 3 bonds trigonal planar ball-and-stick model tin (II) chloride SnCl2 *1200 expanded structural/lewis dot *3 e- pairs and 2 bonds & 1 lone pair trigonal planar coplanar ethene (ethylene) C2 H4 *1200 ball-and-stick model expanded structural condensed structural *coplanar line angel Tetrahedral *109.50 and 4 e- pairs tetrahedron trigonal pyramid bent line 104.5 methane CH4 ammonia NH3 water H 2O Tetrahedral *varies in angle because lone pairs of e’s that are closer to the nucleus have greater repulsive force. *to predict geometries, you need to understand Lewis–dot structures The Shape of Molecules/Molecular orbital treatment and hybridization Shapes of molecules determined by: *VSEPR Theory * molecular orbital treatment & hybridization Molecular orbital treatment & hybridization carbon (excited state) methane CH4 What types of orbitals take part in hydrogen bonding? Molecular orbital treatment & hybridization methane CH4 single bond sp3 is more concentrated in direction than a p orbital *allows more overlapping = stronger bond four sp3 hybrid orbitals hybridization Molecular orbital treatment & hybridization methane CH4 *σ sigma bond describes the molecular orbital *single bonds are sigma bonds Molecular orbital treatment & hybridization carbon (excited state) ethene C2H4 double bond sp2 is more concentrated in direction than a p orbital *allows more overlapping = stronger bond hydrogen Molecular orbital treatment & hybridization ethene C2H4 *σ sigma bond and π bond describes the molecular orbitals *the sp2 bonds is the sigma bond and the regular p orbitals form the π bond. Molecular orbital treatment & hybridization carbon (excited state) ethyne C2H2 triple bond sp is more concentrated in direction than a p orbital *allows more overlapping = stronger bond hydrogen Molecular orbital treatment & hybridization ethyne C2H2 *σ sigma bond and two π bond describes the molecular orbitals *the sp bonds are the sigma bond and two regular p orbitals form the two π bond. Sample Question 1 2 *if it was C1 or 2 the answer is sp2 Sample Question 1 2 Types of formulas wedge diagram ball-and-stick diagram space-filling model Practice