Organic Chemistry Basics

1. Organic Chemistry Basics Chapter 3.1

2. Organic compounds • Carbon covalently bonded to each other and other atoms • Originally thought only to be found in living things • Wide diversity in compounds: more than 5 million have been identified • Macromolecules: cells make large molecules from smaller ones

3. Properties of Carbon • 4 valence electrons = 4 covalent bonds • Can form bonds with itself • Carbon to carbon bonds are strong but not unbreakable, making them good for structural components • Carbon can also form double and triple bonds with itself • Carbon can form straight or branched chains as well as rings

4. Isomers • Compounds with the same molecular formula but different structures • Do not have identical physical or chemical properties • Three types: • Structural – different covalent arrangement • Geometric– different spatial arrangement • Enantiomers– mirror images of each other

5. Structural isomers Geometric isomers Enantiomers

6. Hydrocarbons • Carbon + hydrogen • Nonpolar • Tend to be hydrophobic • Hydrogen atoms can be replaced with a functional group • Polar and ionic functional groups are hydrophilic

7. Functional groups • Hydroxyl group: R-OH • Alcohols • Carbonyl group: carbon to oxygen double bond • Aldehyde: • R-CHO (at end of C skeleton) • Ketone: • R-CO-R (internal carbonyl group) ethanol

8. Functional groups… • Carboxyl group: R-COOH • Amino group: R-NH2 • Both essential in amino acids • Phosphate group: R-PO4H2 • Part of DNA backbone • Sulfhydryl group: R-SH • Thiols – important in proteins

9. Polymers • Formed by linking small organic molecules together • Example: 20 different amino acids form thousands of different proteins • Hydrolysis reactions (‘break with water’) • Breaks apart a polymer • Condensation reactions (‘remove water’) • Joins monomers into a polymer • In biological systems these are regulated by different enzymes.

10. Important Biological Compounds Chapter 3.2-3.5 Overview

11. Carbohydrates • Sugars, starches, cellulose • Carbon, hydrogen, oxygen • (CH2O)n • 2:1 ratio hydrogen to oxygen like water • Monosaccharide – 1 sugar units • Disaccharide – 2 sugar units • Polysaccharides – many sugar units

12. Monosaccharides • 3 – 7 carbon atoms • Hydroxyl group bonded to each C except one; that C double bonded to an O which forms a carbonyl group • Carbons are numbered starting with the C at the carbonyl group

13. Glucose – an important monosaccharide • A hexose (6 C sugar) • Used as an energy source in most organisms – cells oxidize glucose to produce ATP • Glucose is also used to produce amino acids and fatty acids • Is a structural isomer with fructose (found in fruit & honey) • In cells is typically in ring form

14. Disaccharides – 2 monosaccharide units • Maltose (malt sugar) = 2 glucose units • Lactose (milk sugar) = glucose + galactose • Sucrose (table sugar) = glucose + fructose • During digestion these are hydrolyzed to form their monosaccharides

15. Polysaccharides – used for energy storage or structures • Macromolecule – usually glucose units • Starch – energy storage in plants • 2 forms: amylose and amylopectin • Glycogen – ‘animal starch’ – energy storage in animals, especially liver and muscle cells • Cellulose – a structural carbohydrate found in plant cell walls

16. Lipids • Nonpolar • Fats, phospholipids, some cell pigments, steroids, and waxes • Triglyceride – glycerol + 3 fatty acids • Yield more than 2x energy per gram as carbohydrates

17. Saturated vs Unsaturated Fats • Saturatedfatty acids – contain the max number of H atoms • Tend to be solid at room temp • Are associated with increased risk of heart disease • Unsaturatedfatty acids – contain one or more carbon to carbon double bonds • Tend to be liquid at room temp

18. Phospholipids • One end is hydrophobic, one end hydrophilic • This causes them to orient in an aqueous environment with the hydrophobic tails inside a double layer

19. Carotenoids • Orange and yellow plant pigments • In animals these are converted to vitamin A and then to retinal – the visual pigment • Are carrots really good for your eyes??

20. Steroids • Cholesterol – an essential component of animal cells; excess can build up on artery walls and lead to heart disease • Reproductive hormones • Bile salts

21. Important Compounds continued… Chapter 3.3

22. Proteins • Everything the body is and everything the body does • Major structural components of cells • Function as enzymes • Also act in storage, transportation, regulation, motility, and protection • Polymers of amino acids

23. Amino acids • 20 different amino acids • Proteins are chains of amino acids joined by peptide bonds (proteins are sometimes called polypeptides) • The order of amino acids are coded for in DNA • Essential amino acids are those which we must have in our diet because we cannot synthesize them

24. Protein levels of organization • Four levels are related to function • Primary structure: the amino acid sequence • Secondary structure: hydrogen bonding along the backbone • α-helix: coiled protein; found in wool, hair, skin, nails; provides elasticity • β-pleated sheet: strong and flexible but not elastic; silk

25. Organization… • Tertiary structure: 3-D structure controlled by weak interactions along side of protein chains • Quaternary structure: formed when 2 or more polypeptide chains interact

26. Nucleic Acids • Transmit hereditary information • Two classes: DNA and RNA • Polymers of nucleotides: • A 5 carbon sugar (deoxyribose or ribose) • A phosphate group • A nitrogenous base: either a purine (double ring) or a pyrimidine (single ring)  ‘little is double, big is single’ • Adenine, guanine = purine • Cytosine, thymine = pyrimidine • In RNA, thymine is replaced by uracil