ORGANIC CHEMISTRY

1. ORGANIC CHEMISTRY Mr. Dill AP Biology

2. Organic Chemistry • Organic molecules are any molecules that contain atoms from three elements: carbon, hydrogen, and oxygen. • For example, glucose is organic, since its molecular formula is C6H12O6 • Carbon dioxide (CO2) is inorganic since it does not contain hydrogen. • Covalent bonds link carbon atoms together in long chains that form the skeletal framework for organic molecules. These carbon skeletons may vary in: • Length • Shape (straight chain, branched, ring) • Number and location of double bonds • Other elements covalently bonded to available sites

3. All organic molecules have two parts: The carbon backbone & the functional group Tetravalence of carbon allows for complex arrangement of carbon compounds Carbon atoms can form single, double, or triple covalent bonds

4. Name and Comments Space-Filling Model Molecular Formula Structural Formula Ball-and-Stick Model H (a) Methane CH4 C H H H H H (b) Ethane C2H6 C H C H H H H H (c) Ethene (ethylene) C C C2H4 H H • Hydrocarbons • Are molecules consisting of only carbon and hydrogen • Hydrocarbon chains are hydrophobic because the C—C and C—H bonds are nonpolar

5. Fat droplets (stained red) 100 µm (b) Mammalian adipose cells (a) A fat molecule Figure 4.6 A, B Hydrocarbons Found in fossil fuels and makes up the “tails” of lipids

6. Functional Groups groups of atoms acting as a unit,that give organic molecules their physical properties,their chemical reactivity,  &  solubility in aqueous solutions.  most possess electronegative atoms (N, P, O, S...EASILY ATTRACT PROTONS) key bonds are :ester  (C-O-C)  &  amide  (O=C-N-) are ionizable at physiological pH  -NH2AMINE=    amino acid -C=OxCARBONYL=    aldehyde/ketone -COOHxCARBOXYL=    acid -OHxHYDROXYL =    alcohol -PO4PHOSPHORYL=    organic phosphate -SHSULFHYDRYL=    disulfide -CH3METHYL=    hydrocarbon

7. hydroxyl group • Polar group; the bond between the oxygen and hydrogen is a polar covalent bond. • Makes the molecule to which it is attached water soluble. Polar water molecules are attracted to the polar hydroxyl group which can form hydrogen bonds. • Organic compounds with hydroxyl groups are called alcohols.

8. Carbonyl Group • Functional group that consists of a carbon atom double-bonded to oxygen (-C=O) • Is a polar group. The oxygen can be involved in hydrogen bonding, and molecules with his functional group are water soluble. • Is a functional group found in sugars. • Aldehyde = carbonyl group on end carbon of chain • Ketone =- carbonyl group attached to internal carbon

9. Carbonyl Group

10. Carboxyl group Carboxyl Group • Functional group that consists of a carbon atom which is both double-bonded to an oxygen and single-bonded to the oxygen of a hydroxyl group (-COOH). • Is a polar group and water soluble. The covalent bond between oxygen and hydrogen is so polar, that the hydrogen reversibly dissociates as H+. This polarity results from the combined effect of the two electronegative oxygen atoms bonded to the same carbon. • Since it donates protons, this group has acidic properties. Compounds with this functional group are called carboxylic acids.

11. amino group • Functional group that consists of a nitrogen atom bonded to two hydrogen atoms & to the carbon skeleton (—NH2). • Is a polar group and soluble in water. • Acts as a weak base. The unshared pair of electrons on the nitrogen can accept a proton, giving the amino group a +1 charge. • Organic compounds with this function group are called amines.

12. Sulfhydryl group • Functional group which consists of an atom of sulfur bonded to an atom of hydrogen (—SH). • Stabilize the structure of proteins. (Disulfide bridges of proteins) • Organic compounds with this functional group are called thiols.

13. Phosphate group • Functional group which is the dissociated form of phosphoric acid (H3PO4). • Loss of two protons by dissociation leaves the phosphate group with a negative charge. • Has acid properties since it loses protons. • Polar group and soluble in water. • Organic phosphates are important in cellular energy storage and transfer

14. methyl group • methyl group (—CH3) • Non-polar hydrophobic functional group

15. Polymerization • Organic compounds are formed by polymerization • Large carbon compounds are built up from smaller simpler molecules called MONOMERS • Monomers can bind to one another to form complex molecules known as POLYMERS • Macromolecules are very large polymers

16. Polymerization

17. Building and Breaking Polymers • Monomers link to form polymers through a chemical reaction called a CONDENSATION REACTION or Dehydration Synthesis • Water is released during the formation of polymers • The BREAKDOWN of some complex molecules, such as polymers, occurs through a process known as HYDROLYSIS • Hydrolysis is the reversal of a condensation reaction

18. Dehydration Synthesis

19. Hydrolysis

21. 4 Groups of Organic Compounds Found in Living Things • Carbohydrates (C-H-O 1:2:1 ratio) • Lipids (C-H-O) • Proteins (C-H-O-N)…sometimes S • Nucleic Acids (C-H-O-N-P)

23. Carbohydrates • MONOSACCHARIDES are simple sugars in a 1:2:1 ratio • GLUCOSE • GALACTOSE = sugar found in milk • FRUCTOSE = fruit sugar • Chemical composition (C6 H12 O6)

24. Important Monosaccharides Glucose

25. Carbohydrates • DISACCHARIDES consist of two single sugars(monosaccharides) linked together by glycosidic linkage (Dehydration synthesis) • Lactose = Milk sugar • Sucrose = Table sugar

26. Carbohydrates

27. Carbohydrates • POLYSACCHARIDE is a carbohydrate made of long chains of sugars (3 or more monosaccharides) • Starch - Plants convert excess sugars into starches for long-term storage (Alpha linkage) • Glycogen -Animals store glucose in the form of polysaccharide glycogen in the liver and muscles to be used as quick energy • Cellulose -a structural polysaccharide contained in the cell walls of plants (ß linkage) • Chitin – a polysaccharide found in the cell walls of fungi and the exoskeletons of insects and arthropods

29. Starch Glucose

30. Lipids • Lipids are large, NONPOLAR organic molecules that DO NOT dissolve in water • Oils, fats, waxes, and steroids are lipid based • Lipid molecules use less OXYGEN than carbohydrates to store energy efficiently • Used in biological membranes and as chemical messengers • Monomers – Fatty acids & Glycerol

31. Lipids • UNSATURATED FATS are a liquid at room temperature (OILS). Double bonds can have hydrogen added • SATURATED FATS are solid at room temperature NO double bonds

32. Saturated or Unsaturated Fatty Acids Stearic acid Solid at room temp Oleic acid Liquid at room temp

33. Lipids - Saturated and unsaturated

34. Triacylglycerol

35. Phospholipids – Make up the cell membrane

36. Hydrophilic vs Hydrophobic Hydrophilic = Water loving Hydrophobic = Water fearing

37. Proteins • Chemical composition C-H-O-N-S • Proteins are made up of smaller monomers called AMINO ACIDS • Amino Acids differ ONLY in the type of R group they carry Amino acids composed of 3 parts • Amino Group • Carboxylic group • R-group (Makes 20 different amino acids)

39. Peptide Bonds – link amino acids

40. 20 Amino Acids

41. Proteins • Each protein has a specific, and complex shape • Different shapes allow proteins to perform different functions • Two Amino Acids bond to form a DIPEPTIDE during a condensation reaction (2 Amino Acids form a covalent bond, called a PEPTIDE BOND) • Amino Acids can bond to each other one at a time, forming a long chain called a POLYPEPTIDE. • Proteins are composed of one or more polypeptides.

42. Protein Conformation Primary Structure – sequence of amino acids Secondary structure – Folding and coiling due to H bond formation between carboxyl and amino groups of non-adjacent amino acid. R groups are NOT involved. Tertiary structure – disulfide bridges, ionic bonding, or h-bonding of R-groups Quaternary structure – 2+ amino acid chains R- group interactions, H bonds, ionic interactions

43. Primary Structure

44. Secondary Structure

45. Tertiary Structure

46. Quaternary Structure

47. Chaperonins

48. Amino Acids • Amino acid structure: NH3 - C - COOH • Amino acids differ due to the R group • The structure of the R-group determines the chemical properties of the amino acid

49. Amino Acids The polar uncharged amino acids are hydrophilic & can form h-bonds • Serine • Threonine • Glutamine • Asparagine • Tyrosine • Cysteine

50. Amino Acids The nonpolar amino acids are hydrophobic and are usually found in the center of the protein. They also found in proteins which are associated with cell membranes. • Glycine • Alanine • Valine • Leucine • Isoleucine • Methionine • Phenylalanine • Tryptophan • Proline)