WEEK 3

1. WEEK 3 Water pH Organic Chemistry

2. Week 2 Compounds are made up of molecules Molecules are made up of elements Elements are made up of atoms Atoms are made up of protons, neutrons and electrons Elements have properties and are grouped based on these properties in the periodic table of elements

3. Inorganic v Organic Molecules Inorganic • May contain + and – ions • Usually ionic bonding • Small number of atoms • Mostly associated with non-living matter • Organic • Always contain C and H • Always covalent bonding • Often with many atoms and large • Usually associated living • organisms

4. Chemistry of Water Water is made up of 2 hydrogen atoms and 1 oxygen atom, H2O The atoms are held together by hydrogen bonds This hydrogen bonding gives water and other biologically important molecules a specific structure which is essential for proper function

5. Electronegativity of Water Oxygen is more electronegative than Hydrogen It has a greater tendency to gain electrons Oxygen in a water molecule has a partially negative charge Hydrogen in a water molecule has partially positive charges

6. Hydrogen Bonds Hydrogen bonds form when an attractive intermolecular force is created between a hydrogen atom and an electronegative atom Water is a perfect example of hydrogen bonds in action Hydrogen bonds are not the strongest kind of bond between two atoms, however several hydrogen bonds can be very strong Hydrogen bonds hold DNA together

7. Hydrogen bonds and Biomolecules

8. Properties of Water 1- Water has a high heat capacity 2- Water is important for measuring calories 3- Water has a high heat of evaporation 4- Water is a solvent 5- Water molecules are cohesive and adhesive 6- Frozen water is less dense than liquid water

9. Bonding Energy • All bonds posses energy • The amount of energy or heat required to change the temperature is referred to as heat capacity • H2O has a very high heat capacity due to the large numbers of hydrogen bonds • Hydrogen bonds absorb more heat than other types of bonds, therefore hydrogen bonds take much longer to break and need lots of heat/energy to break

10. What is a calorie? • A calorie is the amount of heat energy required to raise the temperature of 1g of H20 by 1° C and is essentially a unit of heat • 1 Calorie = 4.184 Joules (a Joule is a measure of energy) • Hydrogen bonds between water molecules hold more heat than other bonds, therefore water temps fall more slowly than other liquids and this works to protect and maintain homeostasis • This protects organisms from rapid temperature changes

11. Break Out Session You are what you eat…. • McDonald's Big Xtra meal-This meal contains: • 710 calories in the sandwich • 540 calories in the french fries* • 310 calories in the drink* • Large serving • This totals to 1,560 calories, more than half your • daily intake based on a 2,000 calorie diet!!! How much energy will it take to burn 1,560 calories worth of fast food?

12. Heat of Evaporation • Water has a high heat of evaporation • It takes a lot of heat to break water bonds • Water boils and turns to vapor/ gas • In high heat, organisms sweat. The evaporation of sweat works to cool the body. • Sweating is the body’s effort to release energy as heat

13. The Ocean and Heat Capacity • In summer, the ocean warms up and in winter it cools • This process takes a long time due to the high heat capacity and high heat of evaporation of water • Ex. ocean water is warmest in Aug. and coolest in Jan/Feb 2010 Atlantic Ocean temps, degrees F http://www.nodc.noaa.gov/dsdt/wtg12.html

14. Break out session 2 • According to climatologists, earth will continue to rise in temperature anywhere from 1.1 to 6.4 °C by the end of this century • What role do the ocean and other water bodies play in keeping the earth cool? • How will global warming affect the ocean’s temperature and pH?

15. Water is a Solvent • Water dissolves many substances therefore it is a solvent • The polarity of water enables water to have this property • Solvent= a substance which dissolves a solute (solid, liquid or gas) • Solute = a substance dissolved in fluid (Ex. salt, sugar) • Solution = a mixture containing dissolved substances or solutes

16. How water acts as a solvent • H2O is constantly pulling apart and coming together at any given time as molecules crash into each other and re-form • H2O at any given time is made up of H+, OH- and H2O • Therefore, H2O can react with other molecules and act to dissolve them • In this way, water acts as a solvent

17. Hydrophilic v Hydrophobic • Hydro= water (Greek) • Philic = affinity or attraction (Greek) • Phobic = something feared (Greek) • Substances when in contact with water can be • Hydrophilic or Hydrophobic • Ionized or polar molecules are hydrophilic (water loving) • Non ionized or nonpolar molecules are hydrophobic (water fearing) **This is important because when we talk about the cell and the phospholipid bilayer, certain molecules will be able to pass through the boundary and some will not based upon whether they are hydrophobic or hydrophilic

18. Properties of Water Cont.’d Water molecules are cohesive and adhesive Cohesion- Tendency of water molecules to attract one another Adhesion- Attraction of a water molecule to a non-water molecule Important for transport of water in plants - Due to water’s cohesive nature, tension is created as the water molecules bond together -Water is pulled up through the roots of a tree as water evaporates through the leaves

19. Surface Tension Examples of surface tension in action: Rock skipping Water walking insects Belly flopping Water molecules orient them- selves in one direction at the surface Due to the structure of water, its cohesive properties, and the way in which H2O molecules align when exposed to air, H2O has a high surface tension

20. Water as a solid As temperatures drop below 4 C, H-bonds become more rigid This rigidity allows the bonds to remain in a more ‘open’ position due to the lattice structure that is formed when water freezes Water expands when it freezes making it less dense Frozen water is less dense than liquid water Ice floats to the top of a lake or ocean Water freezes top down and protects aquatic organisms and insulates them in winter

21. Acids and Bases Hydrogen Ion Hydroxide Ion ACID- Molecules that release H+ ions in water when they dissociate Ex. Hydrochloric Acid (HCl) H—Cl  H+ and Cl- in water BASE- Molecules that take up H+ ions and release OH- in water when they dissociate Ex. Sodium Hydroxide (NaOH) NaOH  Na+ and OH- in water • Water dissociates into ions (water ‘ionizes’) H2O or H – O—H  H+ + OH-

22. Acids and Bases BASES Ammonia Milk Baking Soda Soap A base is considered strong if it fully dissociates in water ACIDS Lemon juice Vinegar Tomato juice Coffee An acid is considered strong if it fully dissociates in water

23. pH pH is a measure of the number of free (unbound) H+ ions in a solution pH is used to measure the acidity or basicity of a solution A low pHindicates that the solution is acidic A high pH indicates that the solution is basic The pH scale ranges from 0 - 14

24. pH Scale Acid= pH < 7 Base= pH>7

25. pH Ex. a pH of 6 = 1 x 10-6 moles/liter or .000001 a pH of 7 = 1 x 10-7 moles/liter or .0000001 a pH of 8 = 1 x 10-8 moles/liter or .00000001 • pH is expressed as a negative logarithm of the H+ concentration • Log [H+] • The values range from 0-14 or: 1x 100 moles/liter (most acidic) to 1x 10-14 moles/liter (most basic) One mole of water has 1 x 10 -7 moles/liter of H+ ions and is therefore neutral with a pH of 7 • One mole of water has 1 x 10 -7 moles/liter of H+ ions and is therefore neutral with a pH of 7 • **Remember- On a logarithmic scale, each lower unit has 10 times theamount of hydrogen ions as the next higher pH unit Therefore, a pH of 6 has MORE H+ ions than a pH of 8 and is more ACIDIC

26. Acid deposition • Page 33 in your text • Acid deposition -rain or snow with a pH less than 5 and dry acidic particles that settle on Earth from the atmosphere (ex. Pollutants such as Sulfuric acid from burning of fossil fuels) • Commonly referred to as ‘Acid Rain’

27. Impacts of Acid Rain • Acid rain causes the leaching of aluminum from the soil into lakes. Aluminum converts mercury deposits to methyl mercury which is toxic and accumulates in fish (then we eat them! ) • Acid rain • Damages plant leaves, plants unable to do photosynthesis • Puts stress on plants and makes them more susceptible to disease and pests • Toxins that are leached into the soil can kill vital fungi needed to help plants absorb nutrients

29. Impacts of Acid Rain Impact on Humans: • Inhaling dry acidic particles increases the chance for respiratory illness - Ex. Asthma • Buildings made of limestone or marble break down • Paint on homes and cars will be degraded by acid rain

30. Breakout Session 3 How do you contribute to the acid rain problem? - How does the production of plastic bags, shoes, hair dryers, lawn mowers, PVC, cigarettes and hairspray cause acid rain? - Which country out of the following is the worst offender of international environmental law? United States Brazil Peru China Indonesia Australia Russia Japan India Mexico

31. The ten countries with the worst environmental impact are: Brazil United States China Indonesia Japan Mexico India Russia Australia Peru The rankings, published in the journal PLoS ONE, are based on natural forest loss, habitat conversion, marine captures, fertilizer use, water pollution, carbon emissions and species threat. http://www.smartplanet.com/people/blog/pure-genius/study-us- ranks-among-the-worst-countries-for-environmental-impact/3600/ May 2010

32. Buffers and pH A buffer is a chemical that keeps pH steady and within normal limits in living organisms Buffers work by stabilizing the pH of a solution - Buffers will take up excess H+ or OH- ions - Example Carbonic acid and blood

33. Blood pH 7.4 If blood pH rises to 7.8 alkalosis results, if blood pH lowers to 7 acidosis results (both conditions are life threatening) Carbonic Acid (H2CO3) is present in blood either as carbonic acid or bicarbonate ions to prevent any significant changes in the blood pH HCO3, bicarbonate reduces acidity H2CO3, carbonic acid reduces basidity

34. Blood is Organic Blood is considered organic because it is found in living beings and contains organic molecules

35. Classes of Organic Compounds 1- Carbohydrates 2- Lipids 3- Proteins 4- Nucleic Acids There are thousands of different organic molecules within each of these classes Ex. A bacterial cell can contain 5,000 different kinds of organic molecules

36. Organic Molecules WHY IS CARBON SO SPECIAL?? Organic molecules contain carbon and hydrogen atoms bonded to other atoms Organic molecules contain both H and C

37. Why is Carbon so special? Carbon can form covalent bonds with up to 4 other elements (usually CHNOPS) Carbon atoms can form double or triple bonds with certain atoms (Carbon, Nitrogen) Carbon is important for the formation of hydrocarbons- chains of carbon atoms bonded only to H atoms which can form ringed compounds

38. Examples of Hydrocarbons Cyclohexane Octane Both molecules are made up of only C and H The structure makes them have different functions

39. The Carbon Skeleton Backbones can look similar from molecule to molecule HOW DO WE DISTINGUISH MOLECULES FROM EACH OTHER? The carbon chain of an organic molecule is called a skeleton or backbone

40. Functional Groups Functional Groups when added to the carbon skeleton provides us with thousands of different molecules A functional group is a cluster of specific atoms bonded to the carbon skeleton with characteristic structure and functions

41. Functional Groups Examples: When a hydroxyl group is added to a C chain it forms an alcohol (ex. Ethanol) When a carbonyl group is added to a C chain it forms either an Aldehyde or a Ketone as in Formaldehyde or Acetone When a carboxyl group is added it forms Carboxylic acid, ex. Acetic acid and protein When an amino group is added it forms Amine, ex. Tryptophan and is important for Proteins When a phosphate group is added it forms An organic phosphate, important for DNA and ATP PAGE 39 Sulfhydryl R-SH forms disulfide bonds Found in some amino acids

42. Properties of Functional Groups • Depending on the functional group that attaches to the carbon skeleton, the molecule will either become hydrophilic or hydrophobic • Most hydrocarbons are hydrophobic unless they contain a polar functional group • All of the aforementioned groups are polar (except sulfhydryl groups) and thus create hydrophilic compounds • Ex. Ethyl Alcohol (Ethanol) is hydrophilic (dissolves in water) because the hydroxyl group is polar • Non-polar organic molecules are hydrophobic

43. Case Study: The Carboxyl Group • Organic molecules containing hydroxyl groups are highly polar (--COOH) • They tend to ionize and release hydrogen ions --COOH  ---COO- + H+

44. Isomers Isomers are organic molecules that have identical molecular formulas but a different arrangement of atoms Basically, an isomer is a variation of the molecular structure

45. HOMEWORK • Study for exam • Read notes • Read powerpoints • Review handouts • Review chapters • Review self test questions • Read chapter 4 pages 40-47

46. Your first exam will be administered on Tuesday, February 22.  It will be a combination of multiple choice and short answer questions.  The duration of the exam will be 1 hour and will cover lecture weeks 1, 2 and 3.

47. EXAM I REVIEW Lecture I Darwin- The Origin of Species key ideas Theory of Evolution Descent with Modification Natural Selection History of the earth and geological time scales Kingdoms and Domains Classification and Naming of organisms Ecosystems and Populations Cell History- the origin of cells The hierarchy of life (Atom to biosphere) The Scientific Method

48. Week 1 Key areas to focus on: What were Darwin's key ideas and what evidence did he have to support his theory of Evolution? What is natural selection and what role does competition play in natural selection? How do differences in biogeography cause evolution to occur? Understand the concept of all organisms deriving from a common ancestor and the 3 domains of life on earth. Know the three major hypotheses about the origin of life (Chemical Evolution) Table 18.1, page 326 provides the geologic timescale.  Please know the major events that occurred in each era.  Ex. The Cambrian Explosion.  What is the Cambrian Explosion and why is it of significance? Know the differences between prokaryotic and eukaryotic cells. Which cell structures are found in Prokaryotes, which are found in eukaryotes?

49. EXAM I REVIEW Lecture II Inorganic Chemistry What is an atom, element, molecule? Properties of matter and energy Chemical reactions and activation energy Atomic structure- protons, neutrons and electrons The Periodic Table of Elements- how are elements arranged? Electronegativity Electrons and Energy- Octet Rule Elements, Compounds, Molecules and Mixtures Bonds- Ionic, Nonpolar Covalent and Polar Covalent

50. Week 2 Key areas to focus on: Know what atoms, elements, compounds and molecules are; how are they formed?  Where do elements occur on the periodic table and what does it mean? Periodic Table: Know what is meant by a group (vertical) and a period (horizontal).  Know what groups represent and what periods represent. Isotopes- understand what an isotope is and how they are used in medicine Bohr models and energy.  Know that the closer the electron "shell" is to the nucleus, the more stable it is and why. Valence shells, valence electrons and importance in bonding. THE OCTET RULE! Covalent and Ionic bonding.  Understand why some elements are more prone to give up or to accept electrons based on their electronegativity and placement in the periodic table.