Organic Chemistry Introduction PDF

Organic chemistry-Basics Andreas Yiallouris BSc, MSc, MBA, PhD. FHEA A Brief View of Organic Chemistry Don’t Panic! 2  Learning Objectives Carbon and the Elements of Life Functional Groups What is a molecule? Stereochemistry...

Organic chemistry-Basics Andreas Yiallouris BSc, MSc, MBA, PhD. FHEA A Brief View of Organic Chemistry Don’t Panic! 2  Learning Objectives Carbon and the Elements of Life Functional Groups What is a molecule? Stereochemistry 3  Simple to Complex: Life’s Levels of Organization Our journey begins here.  Overview Carbon and the Elements of Life Functional Groups What is a molecule? Stereochemistry 5  Elements of Life Typical living systems are composed (99% by weight) of six elements: C, H, N, O, P, and S. Seventeen other elements occur in minute quantities or as traces. 6  Organic molecules Chains of carbon atoms with other atoms or groups (“functional groups”) attached. Carbon is tetravalent -can make up to 4 covalent bonds -therefore, suited to making complex molecules Glutamine 7  Carbon is the Basic Building Block of Biomolecules Carbon can form an almost infinite number of compounds as a result of its capacity to make as many as four highly stable bonds. Single bonds, double bonds, and triple bonds. Carbons can be tetrahedral, trigonal or linear. Of the over 7 million chemical compounds that are presently known, over 90% are carbon-containing substances. 8 Tetrahedral carbon 9  Tetrahedral arrangement of carbon with single bonds Geometry of carbon bonding Double bonds are flat 10 Double covalent bonds have restricted rotation 11 Representations of three simple organic molecules 12  Variation in carbon skeletons Length Branching Double bonds Rings 13 Biomolecules are made of carbon, which can make single, double and triple bonds Triple bonds are very rare 14 The “Language” of Biochemistry Names of functional groups High energy bonds 15  Learning Objectives Carbon and the Elements of Life Functional Groups What is a molecule? Stereochemistry 16  Functional groups C H 1. Hydrogen C O-H 2. Hydroxyl H 3. Carbonyl O C C O C C C aldehyde ketone 17  Functional groups, continued 4. Carboxyl O H O- + H + C C O C C O 5. Amino H H + C N H + H+ C N H H 18  Functional groups, continued 6. Phosphate O H O- C O P O C O P O O H O- + 2 H+ 19  Functional groups, continued 7. Sulfhydryl C S-H H-S C Disulfide bonds can link two organic molecules C S-S C + 2H+ 20 Functional groups, naming 21 Functional groups, continued 22 Functional groups, continued 23 Examples for functional groups used in biomolecules 24 Examples for functional groups used in biomolecules 25 26 27  Bond Strengths The greater the energy required for bond dissociation (breakage), the stronger the bond. 28  Learning Objectives Carbon and the Elements of Life Functional Groups What is a molecule? Stereochemistry 29  What is a molecule? The definition of a molecule differs slightly from what you learned in chemistry. 2 or more atoms, covalently bonded in specific proportions according to stoichiometry, with a unique geometry. 30  What is a molecule? Molecule Stoichiometry Geometry cis- C2H2Cl2 Cl Cl dichloroethylene C=C H H Hemoglobin 22 31  Covalent bonding The lightest elements can make strong bonds 32 Valences for the major elements of organic molecules Valence reveals the number of covalent bonds the atom will tend to make 33  Learning Objectives Carbon and the Elements of Life Functional Groups What is a molecule? Stereochemistry 34  Learning Objectives Carbon and the Elements of Life Functional Groups What is a molecule? Stereochemistry – Stoichiometry and geometry – Chiral molecules – Enantiomers and Diastereomers – Fisher Projection 35 Isomerism: Constitutional Isomers and Stereoisomers – Stereoisomers are isomers with the same molecular formula and same connectivity of atoms but different arrangement of atoms in space 36 – Enantiomers: stereoisomers whose molecules are nonsuperposable mirror images – Diastereomers: stereoisomers whose molecules are not mirror images of each other Example: cis and trans double bond isomers Example: cis and trans cycloalkane isomers 37 Enantiomers and Chiral Molecules Chiral molecule – Not superimposable on its mirror image – Can exist as a pair of enantiomers Pair of enantiomers – A chiral molecule and its mirror image Achiral molecule – Superimposable on its mirror image 38 The Biological Importance of Chirality The binding specificity of a chiral receptor site for a chiral molecule is usually only favorable in one way 39 Fischer Projection Formulas – A 2-dimensional representation of chiral molecules Vertical lines represent bonds that project behind the plane of the paper Horizontal lines represent bonds that project out of the plane of the paper 40