The Backbone of Biological Molecules

1. The Backbone of Biological Molecules • Although cells are 70–95% water, the rest consists mostly of carbon-based compounds • Carbon is unparalleled in its ability to form large, complex and diverse molecules • Proteins, lipids, DNA, carbohydrates and other molecules that distinguish living matter are all composed of carbon compounds

2. Organic chemistry is the study of carbon compounds • Organic compounds range from simple molecules to colossal ones • Most organic compounds contain hydrogen atoms in addition to carbon atoms • Vitalism, the idea that organic compounds arise only in organisms, was disproved when chemists synthesized the compounds in the lab

4. EXPERIMENT “Atmosphere” CH4 Water vapor Electrode H2 NH3 Condenser Cooled water containing organic molecules Cold water H2O “sea” Sample for chemical analysis

5. Carbon atoms can form diverse molecules by bonding to four other atoms • Electron configuration is the key to an atom’s characteristics • Electron configuration determines the kinds and number of bonds an atom will form with other atoms

6. The Formation of Bonds with Carbon • With four valence electrons, carbon can form four covalent bonds with a variety of atoms • This tetravalence makes large, complex molecules possible • In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape • However, when two carbon atoms are joined by a double bond, the molecule has a flat shape

7. Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model Name (a) Methane (b) Ethane (c) Ethene (ethylene)

8. The electron configuration of carbon gives it covalent compatibility with many different elements • The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules

9. Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4)

10. Molecular Diversity Arising from Carbon Skeleton Variation • Carbon chains form the skeletons of most organic molecules • Carbon chains vary in length and shape

11. Propane Ethane Length 2-methylpropane (commonly called isobutane) Butane Branching 1-Butene 2-Butene Double bonds Cyclohexane Benzene Rings

12. Carbon atoms can partner with atoms other than hydrogen; for example: • Carbon dioxide: CO2 • Urea: CO(NH2)2 O = C = O

13. Hydrocarbons • Hydrocarbons are organic molecules consisting of only carbon and hydrogen • Many organic molecules, such as fats, have hydrocarbon components • Hydrocarbons can undergo reactions that release a large amount of energy

14. Fat droplets (stained red) 100 µm A fat molecule Mammalian adipose cells

15. Isomers • Isomers are compounds with the same molecular formula but different structures and properties: • Structural isomers have different covalent arrangements of their atoms • Geometric isomers have the same covalent arrangements but differ in spatial arrangements • Enantiomers are isomers that are mirror images of each other

16. Pentane 2-methyl butane (a) Structural isomers

17. cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. (b) Geometric isomers

18. L isomer D isomer (c) Enantiomers

19. Enantiomers are important in the pharmaceutical industry • Two enantiomers of a drug may have different effects • Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules

20. L-Dopa (effective against Parkinson’s disease) D-Dopa (biologically Inactive)

21. Effective Enantiomer Ineffective Enantiomer Drug Condition Pain; inflammation Ibuprofen S-Ibuprofen R-Ibuprofen Albuterol Asthma R-Albuterol S-Albuterol

22. Functional groups are the parts of molecules involved in chemical reactions • Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it • Certain groups of atoms are often attached to skeletons of organic molecules

23. The Functional Groups Most Important in the Chemistry of Life • Functional groups are the components of organic molecules that are most commonly involved in chemical reactions • The number and arrangement of functional groups give each molecule its unique properties

24. Estradiol Female lion Testosterone Male lion

25. The six functional groups that are most important in the chemistry of life: • Hydroxyl group • Carbonyl group • Carboxyl group • Amino group • Sulfhydryl group • Phosphate group • Methyl group

26. STRUCTURE (may be written HO—) Ethanol, the alcohol present in alcoholic beverages NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Alcohols (their specific names usually end in -ol) Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3).

27. Acetone, the simplest ketone EXAMPLE STRUCTURE Acetone, the simplest ketone Propanal, an aldehyde NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton FUNCTIONAL PROPERTIES Aldehydes if the carbonyl group is at the end of the carbon skeleton A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.

28. EXAMPLE STRUCTURE Acetic acid, which gives vinegar its sour taste FUNCTIONAL PROPERTIES NAME OF COMPOUNDS Has acidic properties because it is a source of hydrogen ions. Carboxylic acids, or organic acids The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example, Acetic acid Acetate ion In cells, found in the ionic form, which is called a carboxylate group.

29. EXAMPLE STRUCTURE Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. FUNCTIONAL PROPERTIES NAME OF COMPOUNDS Acts as a base; can pick up a proton from the surrounding solution: Amine (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions

30. EXAMPLE STRUCTURE (may be written HS—) Ethanethiol NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20). Thiols

31. Methyl group ( CH3) Methylated compound 5-Methyl cytosine, a component of DNA that has been modified by addition of a methyl group

33. Figure 3.21d Hydrogen bond Hydrophobic interactions and van der Waals interactions Disulfide bridge Ionic bond Polypeptide backbone

34. EXAMPLE STRUCTURE Glycerol phosphate NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Makes the molecule of which it is a part an anion (negatively charged ion). Organic phosphates Can transfer energy between organic molecules.

35. Adenine Phosphate groups Ribose

36. ATP: An Important Source of Energy for Cellular Processes • One phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell • ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups

37. Reacts with H2O Energy Adenosine Adenosine P P P P i P P ATP ADP Inorganic phosphate

38. Animations and Videos • Bozeman - Molecules of Life • Bozeman - Biological Molecules • Building Biomolecules • Properties of Biomolecules • Biochemical Pathway • A Biochemical Pathway • Functional Groups – 1 • Functional Groups - 2

39. Animations and Videos • Chapter Quiz Questions – 1 • Chapter Quiz Questions – 2

40. What was the first organic molecule to be synthesized in the laboratory? • ammonium cyanate • hydrogen cyanide • urea • acetic acid • methane

41. What was the first organic molecule to be synthesized in the laboratory? • ammonium cyanate • hydrogen cyanide • urea • acetic acid • methane

42. Carbon is an unusual atom in that it can form multiple bonds. Which statement is NOT true? A carbon-to-carbon cis double bond is the type found in nature and is associated with cardiovascular health. A carbon-to-carbon trans double bond is made artificially in food processing and is associated with poor cardiovascular health. Multiple carbon-to-carbon double bonds located near each other can absorb light, so they are found in molecules in the eye or in chloroplasts. Multiple carbon-to-carbon bonds are stronger than single bonds. Saturated fats are those that have a carbon-to-carbon double bond and are associated with good health.

43. Carbon is an unusual atom in that it can form multiple bonds. Which statement is NOT true? A carbon-to-carbon cis double bond is the type found in nature and is associated with cardiovascular health. A carbon-to-carbon trans double bond is made artificially in food processing and is associated with poor cardiovascular health. Multiple carbon-to-carbon double bonds located near each other can absorb light, so they are found in molecules in the eye or in chloroplasts. Multiple carbon-to-carbon bonds are stronger than single bonds. Saturated fats are those that have a carbon-to-carbon double bond and are associated with good health.

44. What type of chemical bond joins a functional group to the carbon skeleton of a large molecule? • covalent bond • hydrogen bond • ionic bond • double bond • disulfide bond

45. What type of chemical bond joins a functional group to the carbon skeleton of a large molecule? • covalent bond • hydrogen bond • ionic bond • double bond • disulfide bond

46. Which of the following is NOT one of the seven functional groups found in biological molecules? • amino • hydroxyl • carboxyl • cyanate • phosphate

47. Which of the following is NOT one of the seven functional groups found in biological molecules? • amino • hydroxyl • carboxyl • cyanate • phosphate

48. Which functional group behaves as a weak acid in organic molecules? • amino • carboxyl • carbonyl • sulfhydryl • hydroxyl

49. Which functional group behaves as a weak acid in organic molecules? • amino • carboxyl • carbonyl • sulfhydryl • hydroxyl

50. Which functional group behaves as a weak base in organic molecules? • amino • carboxyl • carbonyl • sulfhydryl • hydroxyl