Lecture - 2

1. Lecture - 2 Water & Carbon

2. Quiz Answers • The Carboxyl functional group: • The most predominant color on a world map is blue. • The Central dogma of Molecular Biology is: • DNA → RNA → PROTEIN • Epigenetics: The structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states. • The best part of California is the people!

3. Outline • Water • Structure • Important properties • Carbon • Structure • Important properties • Functional Groups

4. Water • The molecule that supports all life (as we know it) • It is the biological medium on Earth • All living organisms require water • Most cells are surrounded by water, and cells themselves are about 70–95% water • The abundance of water is the main reason the Earth is habitable

5. Water is a polar molecule • Polar covalent bonds allow for extensive hydrogen bonding • Polar – the opposite ends have opposite charges

6. Four Important Properties of Water • Cohesive behavior • Ability to moderate temperature • Expansion upon freezing • Versatility as a solvent

7. #1 - Cohesion • Cohesion • Hydrogen bonds hold water molecules together • Adhesion • An attraction between different substances

8. Example of Cohesion & Adhesion Water molecules bind together to form the water column (cohesion) They also bind to the cell walls to help resist gravity (adhesion)

9. #1 - Cohesion • Surface tension • Related to cohesion • A measure of how hard it is to break the surface of a liquid

10. #2 – Moderation of Temperature • Kinetic energy is the energy of motion • Heat = the total amount of kinetic energy due to molecular motion • Temperature measures the intensity of heat due to the average kinetic energy of molecules

11. #2 – Moderation of Temperature • Measuring temperature • Celsius scale to indicated temperature • 0 degrees Celsius is freezing, 100 degrees is boiling • Room Temp is about 20 - 25 degrees • Why would most biochemical experiments be run at 37 degrees? • Calorie • The amount of heat it takes to raise the temperature of 1g of water by 1 degree celcius

12. #2 – Moderation of Temperature • Specific Heat - The amount of heat that must be absorbed or lost for 1g of substance to change its temperature 1 degree C. • Water has a high specific heat.

13. #2 – Moderation of Temperature • Water has a High Specific Heat • allows it to minimize temperature fluctuations • Heat is absorbed when hydrogen bonds break • Example: Liquid water  steam • Heat is released when hydrogen bonds form • Water vapor in clouds  raindrops • Formation of raindrops or ice actually raises the surrounding air temperature by a slight amount!

14. #2 - Moderation of Temperature • Oceans stabilize the temperature of the air. • Water absorbs heat from warmer air and releases stored heat to cooler air • Water can absorb or release a large amount of heat with only a slight change in its own temperature

15. #2 – Moderation of Temperature • Oceans can absorb heat during the day and release it back at night while the ocean temp remains relatively constant. San Bernardino 100° Burbank 90° Santa Barbara 73° Riverside 96° Los Angeles (Airport) 75° Santa Ana 84° Palm Springs 106° 70s (°F) 80s Pacific Ocean 68° 90s 100s 40 miles San Diego 72°

16. #2 – Moderation of Temperature • Evaporation is transformation of a substance from liquid to gas • Heat of vaporization • The heat a liquid must absorb for 1 g to be converted to gas – water has a high heat of vaporization • As a liquid evaporates, its remaining surface cools, a process called evaporative cooling • Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water

17. # 3 – Expansion Upon Freezing • Ice Floats on Water • As H-bonds stabilize, the resulting crystal becomes less dense. • H-bonds are breaking and re-forming in liquid water, therefore there are more molecules per volume

18. #3 – Expansion Upon Freezing Hydrogen bond Liquid water: Hydrogen bonds break and re-form Ice: Hydrogen bonds are stable

19. #3 – Expansion Upon Freezing • Major benefit of Ice floating on water – Insulation • Insulates living organisms under ice pack in lakes and frozen seas. • Snow insulates seeds and roots under ground in winter.

20. Figure 3.7 #4 – Solvent Properties  Na     • Water is a versatile solvent due to its polarity • It can easily for hydrogen bonds with other molecules including ionic compounds    Na    Cl Cl        

21. Figure 3.8 #4 – Solvent Properties • Large molecules such as proteins can dissolve in water if they have ionic and polar regions +      + 

22. #4 – Solvent Properties • Hydrophilic - substance that has an affinity for water. • Hydrophobic – substance that does not have an affinity for water. • Some molecules are both.

23. #4 – Solvent Properties • Water can disassociate into hydronium and hydroxide ions +  2 H2O Hydronium ion (H3O+) Hydroxide ion (OH)

24. #4 Solvent Properties: Acids & Bases • The dissociation of water molecules has a great effect on organisms • Changes in concentrations of H+ and OH– can drastically affect the chemistry of a cell

25. #4 Solvent Properties: Acids & Bases • Acid – • donates a proton • Increases the number of Hydronium Ions in an aqueous solution • Base – • Accepts a proton • Reduces the number of Hydronium Ions in an aqueous solution

26. #4 – Solvent Properties: The pH scale • pH is a measure of the relative concentration of protons. • 0 < pH < 7 is an Acid ([H30+] > 10-7M) • 7 < pH < 14 is a Base ([H30+] < 10-7M) • pH 7 is neutral ([H30+] = [OH-] = 10-7M)

27. Figure 3.10 pH Scale 0 1 Battery acid 2 Gastric juice, lemon juice H+ H+ H+ Vinegar, wine, cola OH 3 H+ Increasingly Acidic [H+] > [OH] H+ OH H+ H+ H+ 4 Tomato juice Acidic solution Beer Black coffee 5 Rainwater 6 Urine OH Saliva Neutral [H+] = [OH] OH 7 Pure water OH H+ H+ OH OH Human blood, tears H+ H+ H+ 8 Seawater Neutral solution Inside of small intestine 9 10 Increasingly Basic [H+] < [OH] Milk of magnesia OH OH 11 OH H+ OH Household ammonia OH OH OH H+ 12 Basic solution Household bleach 13 Oven cleaner 14

28. #4 – Solvent Properties: Buffers • Buffers are substances that minimize changes in concentrations of H+ and OH– in a solution. • They resist a change in pH when a small amount of acid or base is added to a solution. • Most buffers consist of an acid-base pair that reversibly combines with H+ • Buffers work within a specific pH range.

29. #4 – Solvent Properties: Buffers • Carbonic Acid – contributes to pH stability in blood and other biological solutions. • H2CO3 is formed when CO2 reacts with water.

30. Carbon

31. Carbon • The backbone of life • Living organisms consist mostly of carbon-based compounds. • Really good at forming large, complex, and diverse molecules. • Proteins, DNA, carbohydrates, and other molecules - all composed of carbon compounds.

32. Carbon • Electron configuration determines the kinds and number of bonds an atom will form with other atoms • Four valence electrons – Four covalent • Allows for the formation of large, complex molecules possible

33. Figure 4.3 Carbon bonds determine molecular shape Name andComment Structural Formula Space-Filling Model Molecular Formula Ball-and- Stick Model (a) Methane CH4 (b) Ethane C2H6 (c) Ethene (ethylene) C2H4

34. Figure 4.5 Diversity of carbon molecules (c) Double bond position (a) Length • Carbon chains form the skeletons of most organic molecules • Carbon chains vary in length and shape Ethane Propane 2-Butene 1-Butene (b) Branching (d) Presence of rings Benzene 2-Methylpropane (isobutane) Butane Cyclohexane

35. Figure 4.4 Valence Electrons • 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 Oxygen (valence  2) Hydrogen (valence  1) Nitrogen (valence  3) Carbon (valence  4)

36. Isomers • Compounds with the same molecular formula but different structures and properties • Structural isomers have different covalent arrangements of their atoms (constitutional) • Cis-trans isomers have the same covalent bonds but differ in spatial arrangements • Enantiomers are isomers that are mirror images of each other (they are chiral)

37. (a) Structural isomers Isomers – Three types Figure 4.7 (b) Cis-trans isomers cis isomer: The two Xsare on the same side. trans isomer: The two Xsare on opposite sides. (c) Enantiomers CO2H CO2H H NH2 H NH2 CH3 CH3 L isomer D isomer

38. Figure 4.8 Isomers - Enatomers Ineffective Enantiomer Effective Enantiomer Drug Condition Pain;inflammation Ibuprofen S-Ibuprofen R-Ibuprofen Albuterol Asthma R-Albuterol S-Albuterol http://www.youtube.com/watch?v=L5QbBYj_zVs

39. Functional Groups • 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

40. Female lion OH CH3 HO Estradiol Male lion OH CH3 CH3 O Testosterone The importance of functional groups

41. 7 most biologically important functional groups

42. Figure 4.9a Hydroxyl STRUCTURE Alcohols (Their specific names usually end in -ol.) NAME OF COMPOUND (may be written HO—) • Is polar as a result of the electrons spending more time near the electronegative oxygen atom. EXAMPLE FUNCTIONALPROPERTIES Ethanol • Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

43. Figure 4.9b Carbonyl STRUCTURE Ketones if the carbonyl group is within a carbon skeleton NAME OF COMPOUND Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE • A ketone and an • aldehyde may be • structural isomers • with different properties, • as is the case for • acetone and propanal. FUNCTIONALPROPERTIES • Ketone and aldehyde • groups are also found • in sugars, giving rise • to two major groups • of sugars: ketoses • (containing ketone • groups) and aldoses • (containing aldehyde • groups). Acetone Propanal

44. Figure 4.9c Carboxyl STRUCTURE Carboxylic acids, or organic acids NAME OF COMPOUND EXAMPLE FUNCTIONALPROPERTIES Polar; can form H-bonds Weak acids; reversible dissociation in H2O Acetic acid Nonionized Ionized • Found in cells in the ionized form with a charge of 1– and called a carboxylate ion.

45. Figure 4.9d Amino Amines STRUCTURE NAME OF COMPOUND •Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms): EXAMPLE FUNCTIONALPROPERTIES Glycine Ionized Nonionized •Found in cells in the ionized form with a charge of 1.

46. Figure 4.9e Sulfhydryl Thiols STRUCTURE NAME OF COMPOUND (may be written HS—) •Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. EXAMPLE FUNCTIONALPROPERTIES •Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers and then breaking and re-forming the cross-linking bonds. Cysteine

47. Figure 4.9f Phosphate Organic phosphates STRUCTURE NAME OF COMPOUND EXAMPLE •Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule, as at left; 1– when located internally in a chain of phosphates). FUNCTIONALPROPERTIES Glycerol phosphate •Molecules containing phosphate groups have the potential to react with water, releasing energy.

48. Figure 4.9g Methyl STRUCTURE Methylated compounds NAME OF COMPOUND •Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes. EXAMPLE FUNCTIONALPROPERTIES •Arrangement of methyl groups in male and female sex hormones affects their shape and function. 5-Methyl cytidine