CHAPTER 2 The Chemical Basis of Life

1. CHAPTER 2The Chemical Basis of Life Modules 2.9 – 2.17

2. THE PROPERTIES OF WATER 2.9 Water is a polar molecule • Atoms in a covalently bonded molecule may share electrons equally, creating a nonpolar molecule • If electrons are shared unequally, a polar molecule is created

3. A Nonpolar Molecule is a system in which the net partial positive charge and net partial negative charge occur at the same location and effectively cancel each other out. Nonpolar systems are usually characterized as having high levels of symmetry overall.

4. This makes the oxygen end of the molecule slightly negatively charged • The hydrogen end of the molecule is slightly positively charged • Water is therefore a polar molecule • In a water molecule, oxygen exerts a stronger pull on the shared electrons than hydrogen (–) (–) O H H (+) (+) Figure 2.9

5. 2.10 Overview: Water’s polarity leads to hydrogen bonding and other unusual properties • The charged regions on water molecules are attracted to the oppositely charged regions on nearby molecules • This attraction forms weak bonds called hydrogen bonds (H and N,O H) • So…why is water wonderful??????? Hydrogen bond Figure 2.10A

6. Because of Hydrogen Bonds • A hydrogen bondis the force of attraction between a hydrogen molecule with a partial positive charge and another atom or molecule with a partial or full negative charge.

7. “A hydrogen bond is a special type of bond that exists between an electronegative atom and a hydrogen atom bonded to another electronegative atom. This type of bond always involves a hydrogen atom, thus the name. Hydrogen bonds can occur between molecules (intermolecularly), or within different parts of a single molecule (intramolecularly). The typical hydrogen bond is stronger than van der waals, but weaker than covallent, ionic and metallic bonds.” http://en.wikipedia.org/wiki/Hydrogen_bond

8. Electronegativities

9. “Hydrogen bonding also plays an important role in determining the three-dimensional structures adopted by proteins and nucleic bases. In these macromolecules, bonding between parts of the same macromolecule cause it to fold into a specific shape, which helps determine the molecule's physiological or biochemical role. The double helical structure of DNA, for example, is due largely to hydrogen bonding between the base pairs, which link one complementary strand to the other and enable replication.” http://en.wikipedia.org/wiki/Hydrogen_bond

10. So…what else is so wonderful about water??????? • 1. Like no other common substance, water exists in nature in all three physical states: • as a solid • as a liquid • as a gas Figure 2.10B

11. 2. Hydrogen bonds make liquid water cohesive • Due to hydrogen bonding, water molecules can move from a plant’s roots to its leaves (adhesion) • Insects can walk on water due to surface tension created by cohesive water molecules (cohesion) Figure 2.11

12. Surface Tension • At the surface of the liquid, the molecules are pulled inwards by other molecules deeper inside the liquid but they are not attracted as intensely by the molecules in the neighboring medium (be it vacuum, air or another liquid). Therefore all of the molecules at the surface are subject to an inward force of molecular attraction which can be balanced only by the resistance of the liquid to compression.

14. 3. Water’s hydrogen bonds moderate temperature • It takes a lot of energy to disrupt hydrogen bonds • Therefore water is able to absorb a great deal of heat energy without a large increase in temperature(summer ocean) • As water cools, a slight drop in temperature releases a large amount of heat(coastal climate) • The specific heat of water is 1 calorie/gram °C = 4.186 joule/gram °C which is higher than any other common substance (Aluminum .22 calorie/gram °C). • The specific heat is the amount of heat per unit mass required to raise the temperature by one degree Celsius.

15. Prevailing Wind Patterns

16. 4. Water has a high heat of vaporization (539 cal/gram). This leads to evaporative cooling • A water molecule takes a large amount of heat energy with it when it evaporates The energy required to change a gram of a liquid into the gaseous state at the boiling point is called the "heat of vaporization". Figure 2.12

17. 5. Ice is less dense than liquid water • Molecules in ice are farther apart than those in liquid water Hydrogen bond ICE Hydrogen bonds are stable LIQUID WATER Hydrogen bonds constantly break and re-form Figure 2.13

18. If ice sank, it would seldom have a chance to thaw • Ponds, lakes, and oceans would eventually freeze solid • The temperature of the water at the bottom of Lake Erie on January 1, 1900 was 4 degrees Celsius. It will be the same on January 1, 2012. • Ice is therefore less dense than liquid water, which causes it to float

19. Ice, molecular model • Ice, molecular model

20. Water, molecular model

21. As ice thaws, collapsing crystals decrease in volume until the effect of greater molecular motion takes over. At that point the water’s volume expands with increasing temperature. Expansion of Water Volume 1.0006 0 4 8 12 16 18 Temperature degrees C

22. The collapsing of ice crystals plus increased molecular motion with increasing temperature produce the overall effect of water being most dense at 4 degrees C.

23. As water is cooled, it sinks until the entire pond is 4°C. Only then can surface cooling to the freezing point take place without further sinking

24. 6. Water is a versatile solvent • Solutes whose charges or polarity allow them to stick to water molecules dissolve in water • They form aqueous solutions ex. NaCl Na+ – – Na+ + + Cl– Cl– – – + + – Ions in solution Salt crystal Figure 2.14

25.   Due to the polarity of water, H end of water nearest Cl – and O side of water nearest Na + .

26. Solutions which contain water are extremely important in biology. • When compounds are mixed together, and they retain their chemical properties, they are called mixtures. There are three types of mixtures: solutions, suspensions, and colloids. • Solutions, suspensions, and colloids which include water are extremely important in biology.

27. Solutions Important in Biology • Solution- one or more substances uniformly distributed in another substance. • Solute= NaCl • Solvent = water • Concentration= amount of solute dissolved in a fixed amount of solvent • Ex. Aqueous solutions important in biology: nutrients dissolved in sea water to marine organisms, plant nutrients dissolved in rain water, gases and ions dissolved in plasma

28. Suspensions Important in Biology • Suspension- A mixture in which the particles spread throughout a liquid or a gas but settle out over time. • Suspensions important in biology: sand in water, rbc and wbc in blood (5Liters)

29. Colloids Important in biology • Colloid- a mixture of particles that do not settle out over time, but are intermediate in size between a solution and a suspension. • Colloids important in biology= fat in milk, mayonnaise, jello, smoke, dyes, whipped cream, cytoplasm of cells ex. amoeba • The fat content in the upper 100 mL of a liter of milk can not differ by more than 10% from the rest of the milk (Dept. of Health) (homogenization).

30. Homogenization breaks up the milk fat globules so they are nearly the same size.

31. States of colloids: gel is a semisolid colloid and sol is a liquid colloid ex. Amoeba gel and sol http://video.google.com/videoplay?docid=6605346366794347685&q=amoeba+engulfing&total=1&start=0&num=10&so=0&type=search&plindex=0

32. Back to: Aqueous solutions which are extremely important in biology. • At room temperature, one in a billion water molecules will ionize: • H2O(l) <-> H+(aq) + OH-(aq) • An H+ ion is a hydrogen atom that has lost its (one and only) valence electron. In other words, it is a naked proton. This proton is quite reactive. Hydronium ion

33. The H3O+(aq) ion is called a hydronium ion Chemists use H+ and H3O+ terms interchangeably to represent the hydrated proton in acidic aqueous solutions. This property of water along with its solute helps to determine if a solution is acidic, basic or neutral. ditto ditto

34. The chemistry of life is sensitive to acidic and basic conditions • An acid produces hydrogen ions in solution because it reacts with the water molecules by giving a proton to them (Arrhenius and Bronsted Lowry). • A chemical compound that donates H+ in solution is an acid (Lewis).

35. The strength of an acid is based on the concentration of H+ ions in the solution. The more H+the stronger the acid.Example: HCl (Hydrochloric acid) in water • Characteristics of Acids:**Acids taste sour**Acids react strongly with metals (Zn + HCl)**Strong Acids are dangerous and can burn your skinExamples of Acids:1. Vinegar 2. Stomach Acid (HCl) 3. Citrus Fruits

36. Bases are substances which produce hydroxide ions in solution(Arrhenius and Bronsted Lowry). A base is a compound that accepts H+ ions and removes them from solution (Lewis).

37. Bases are compounds that break apart to form a negatively charged hydroxide ions (OH-) in water. The strength of a base is determined by the concentration of Hydroxide ions (OH-). The greater the concentration of OH- ions the stronger the base.Example: NaOH (Sodium Hydroxide-a strong base) in water Solutions containing bases are often called alkaline.Characteristics of Bases:**Bases taste bitter**Bases feel slippery**Strong bases are very dangerous and can burn your skinExamples:1. lye (Sodium Hydroxide)2. Ammonia

38. pH scale H+ OH– Lemon juice; gastric juice Increasingly ACIDIC (Higher concentration of H+) Grapefruit juice • The pH scale Acidic solution Tomato juice Urine NEUTRAL [H+] = [OH–] PURE WATER Human blood Seawater Neutral solution Increasingly BASIC (Lower concentration of H+) Milk of magnesia Household ammonia Household bleach Oven cleaner Basic solution Figure 2.15

39. What is pH? The number…. • pH is defined mathematically as the negative logarithm (base 10) of the H3O+ (H+) concentration. PH values are calculated in powers of 10. The hydrogen ion concentration of a solution with a pH of 1.0 is 10 greater than a solution with a pH of 2.0. The greater the hydrogen ion concentration, the lower the pH; when the pH is above 7, the solution is basic (alkaline), and when it is below 7, the solution is acidic.

40. How is this relevant to our bodies? • Your body must maintain homeostasis-adjustment to the internal environment to maintain constant conditions • For example, cells are kept close to pH 7 by buffers. • Buffers are substances that resist pH change • They accept H+ ions when they are in excess and donate H+ ions when they are depleted • The blood buffer system assures the healthy pH of our blood.

41. Blood Buffer System C6H12O6 + 6O2 ---->  6CO2 + 6H2O

42. The Blood Buffer System • The bicarbonate buffering system is important in many different cellular processes. Just a few are listed below. • It is one of the major buffering systems used to maintain the pH of mammalian blood.The pH of blood can not differ more than 7.35-7.45 or death will ensue. • It is used in the formation of acid in the lumen on the stomach. • It is used to neutralize the pH of the chyme leaving the stomach and entering the small intestine.

43. When carbon dioxide dissolves in water, it can do so as a gas dissolved in water or by reacting with water to produce carbonic acid. In the cells of your body, the rate of carbonic acid production is accelerated by the enzyme carbonic anhydrase, as indicated in the following figure. • Carbonic acid is known as a weak acid because it partially dissociates into the positive Hydrogen ions and negative bicarbonate ions.

44. For example, when excess hydrogen ions are added to the system the equilibrium is shifted to the left. This means that some of the added hydrogen ions will react with the bicarbonate ions to produce carbonic acid and the carbonic acid will dissociate into carbon dioxide and water as shown below.

45. When hydrogen ions are removed from the reaction, the equilibrium will shift to the right. More carbon dioxide will combine with water and more carbonic acid will be produced and more hydrogen ions and bicarbonate ions will be produced.

47. pH is very important in DigestionpH is very important in drug Pharmaco-kinetics and pharmaco-dynamics

48. Antacids---Magnesium Hydroxide and Aluminum Hydroxide

49. Proton Pump Inhibitors--Omeprazole

50. Acid precipitation threatens the environment • Some ecosystems are threatened by acid precipitation • Acid precipitation is formed when air pollutants from burning fossil fuels combine with water vapor in the air to form sulfuric and nitric acids Figure 2.16A