CEE 210 Environmental Biology for Engineers

1. Lecture 1: Biochemistry Basics CEE 210 Environmental Biology for Engineers Instructor: L.R. Chevalier Department of Civil and Environmental Engineering Southern Illinois University Carbondale

2. Objectives • Review basic chemistry of small molecules • Review the basic atom • Understand the orbital structure of the atom • Review how a periodic table is organized • Understand covalent, ionic and hydrogen bonding • Review the definition of pH • Survey the properties of water • Review major concepts in organic chemistry

3. Example of Biochemistry • Biology and medicine have enjoyed enormous benefit from a biochemical approach to life • One striking example uses the fact that spinning nuclear protons can be regarded as simple magnets, and interact with an external magnetic field • MRI scans, such as this one of the human head, uses technology based on these principles. The technology produced high quality images of soft tissue

4. Basic Chemistry of Small Molecules • Names of the elements are abbreviated. • Often, the abbreviation makes perfect sense (C for carbon) • Sometimes it does not (Na for sodium). • There is an abundance of elements on earth and in living systems • 4 elements make up 99% of living organisms. • oxygen (O) • carbon (C) • hydrogen (H) • nitrogen (N)

5. Terms to know • Element • matter composed of atoms that all have the same atomic number (protons). • Atom • the smallest component of an element that still has properties of the element • positively charged nucleus surrounded by a charged cloud of electrons • "+" and "-" charges strongly attract • Proton • particle in the nucleus with a positive charge of +1 and an atomic mass number of 1 Dalton. • Neutron • a non-charged nuclear particle with the same mass as the proton. • Electron • negatively charged particle (-1) with a mass 1/1837 of that of a proton. • Isotope • atoms with the same number of protons and electrons, but different numbers of neutrons. • Atomic number • number of electrons • number of protons 26 Fe 55.85 Symbol/name Atomic Mass - in amu (atomic mass units)

6. Basic Atom ______ (positive) Nucleus ________ (negative) _____________ (neutral)

7. The Electron • Electrons determine chemical properties of elements • Electrons are outside the nucleus • Chemical reactions involve sharing or exchanging electrons • Electrons move about the nucleus in atomic orbitals • The atom is stable when the outermost energy level of most atoms has eight electrons • Stability can be achieved by adding, losing, or sharing electrons

8. Orbital Structure Carbon (Atomic Number 6) Oxygen (Atomic Number 8) 6p 6n 8p 8n 4p 3d 4s 3p 3s Energy Hund’s Law (not to scale) 2n2 electrons fill each orbit (n is the # before the letter) Note that 4s has lower energy than 3d This orbit fills first. 2p 2s 1s

9. Orbital Structure Carbon (Atomic Number 6) Oxygen (Atomic Number 8) 6p 6n 8p 8n 4p 3d 4s 3p 3s Also represented as 1s22s22p2 1s22s22p4 Energy 2p 2s 1s 1s 2s 2s 2p 2p 3s 3s 3p 3p 1s

10. Periodic Table • Atomic number • number of electrons • number of protons 26 Fe 55.85 Symbol/name Atomic Mass - in amu (atomic mass units)

11. Periodic Table In the periodic table, elements have something in common if they are in the same row. All of the elements in a row, or period, have the same number of __________. Every element in the top row (the first period) has ____ orbital for its electrons. All of the elements in the second row (the second period) have _____ orbitals for their electrons. It goes down the periodic table like that.

12. Periodic Table When a column goes from top to bottom, it's called a group. The elements in a group have the same number of ___________________________________________ Every element in the first column (group one) has one _________ in its outer shell. Every element on the second column (group two) has two ________ in the outer shell. As you keep counting the columns, you'll know how many _______ are in the outer shell. There are some exceptions to the order when you look at the transition elements, but you get the general idea.

13. Covalent Bonding:Biologically important chemicals 7p 7n Nitrogen (Atomic Number 7)

14. Covalent Bond of Chemicals • Sharing electrons leads to the formation of covalent bonds • Bonds contain energy, and a require energy to be broken • Bond energy (expressed as kcal/mole) is the energy required to break a bond • For example, an H-H bond requires 104 kcal/mole to break

15. Example of Covalent Bond: Methane, CH4 6p 6n 6p 6n 1p 1n 1p 1n 1p 1n 1p 1n 1p 1n

16. Example of Covalent Bond: Methane H H C H H C C

17. Example of a Double Covalent Bond: Oxygen

18. Quick Quiz • Provide the following information for silicone • Symbol • Atomic number • Atomic mass • Number of electrons, protons and neutrons • What is the electron configuration of • Boron • Magnesium • In covalent bonding, which of the following statements are true? • Two molecules share electrons in their outer orbitals • Hydrogen must be present • Carbon must be present • The bond is highly unstable

19. Ionic Bonding • Ions are produced when atoms can obtain a stable number of electrons by ______________electrons • For example Na (sodium) can donate an electron to Cl (chlorine) generating Na+ and Cl-. • The ion pair is held together by strong electrostatic attractions • In general, covalent bonds are stronger

20. Ionic Bonding Na Cl 11p 11n 17p 17n Cl- Na+

21. Water • 70% of the Earth's surface is covered with this simple molecule • Scientists estimate that the hydrosphere contains about 1.36 billion cubic kilometers of this substance mostly in the form of a liquid (water) that occupies topographic depressions on the Earth • The second most common form of the water molecule on our planet is ice • If all our planet's ice melted, sea-level would rise by about ____ meters • Water is also essential for life • Most animals and plants contain more than 60% water by volume • Without water life would probably never have developed on our planet

22. Covalent Bonding of Water H2O 8p 8n These three nuclei and 10 electrons possess properties that make it the most unique of more than 15 million chemicals we presently know 1p 1n 1p 1n

23. Polarity of Water H2O + - 8p 8n The four electrons surrounding the oxygen ten to arrange themselves at one side of the molecule, giving the molecule a positive and negative end. 1p 1n 1p 1n

24. Hydrogen Bonding of Water Molecules • As stated in the previous slide, the water molecule has a negative charge and a positive charge on either end • The resulting polarity of charge causes molecules of water to be attracted to each other forming molecular bonds • Hydrogen bonding is not as strong as covalent bond, but it is responsible for the unique properties of water + + + H H H H H H O O O - - - -

25. Hydrogen Bonding of Water Molecules

26. Water: The Major Biological Solvent • Water dissolves compounds by separating them into their individual compounds • Consider the illustration below • Sodium chloride (NaCl) is shown in its crystalline form (left) • Then dissolved in water (right) - + - - - + + + - + + + + + + + + + - + + + + + + + + - - - - - - - - + - - + Chlorine (Cl-) + Sodium (Na+)

27. Water: The Major Biological Solvent

28. Water: What is pH? • Sometimes one of the ions is • H+ • OH- • The addition of these ions changes the pH of the water • We define the pH of a solution as the negative logarithm of the hydrogen ion concentration. • pH 7.0, a solution is neutral • lower pH (1-6), a solution is acidic • higher pH (8-14), a solution is basic

29. Example of adding an acid or a base • Hydrochloric acid dissolves in water • Sodium hydroxide dissolves in water

30. Examples of pH values Source http://www.visionlearning.com Library>Chemistry>Acid and Bases

31. Acid-Base Reactions • Governing equation • HA H+ + A- • where HA is the acid • A- is the conjugate base • where Ka is the acid dissociation constant • Note: [ ] designates moles/liter

32. Acid-Base Reactions • Just like the pH, the pKa tells you of the acid or basic properties of a substance • pKa <2 means strong acid • pKa >2 but < 7 means weak acid • pKa >7 but <10 means weak base • pKa >10 means strong base

33. Acid-Base Reactions

34. Water – Unique Properties • Water is a universal solvent • It is able to dissolve a large number of different chemical compounds • This feature also enables water to dissolve and carry nutrients in plants and living organisms, and to eliminate waste • Water is one of natures most stable molecules • Water in a pure state has a neutral pH • Pure water is neither acidic nor basic • pH changes when substances are dissolved in it • Water molecules are the only substance on Earth that exist in all three physical states of matter: solid, liquid, and gas

35. Water – Unique Properties • Water molecules exist in liquid form over an important range of temperature from 0 - 100° Celsius. • This range allows water molecules to exist as a liquid in most places on our planet • Water has a high surface tension • This phenomenon also causes water to stick to the sides of vertical structures despite gravity's downward pull. • Water's high surface tension allows for the formation of water droplets and waves, allows plants to move water (and dissolved nutrients) from their roots to their leaves, and the movement of blood through tiny vessels in the bodies of some animals.

36. Water – Surface Tension

37. Water – Unique Properties • The freezing of water molecules causes their mass to occupy a larger volume. • When water freezes it expands rapidly adding about 9% by volume. • Fresh water has a maximum density at around 4° Celsius. • Water is the only substance on this planet where the maximum density of its mass does not occur when it becomes solidified.

38. Carbon - The essential element Carbon (Atomic Number 6) 6p 6n Organic molecules contain carbon backbones. Every carbon atom will form 4 covalent bonds with other atoms, specifically other carbon atoms as well as hydrogen, nitrogen, oxygen and sulfur atoms. By linking together of many smaller molecules, carbon is able to form very large polymers (macromolecules) many of which are important to human physiology.

39. Organic Chemistry Primer • Organic molecules contain both carbon and hydrogen • May contain other elements • However the carbon-hydrogen bond defines them as organics • Organic chemistry defines life • Millions of different types of living organisms • Million of different organic molecules with unique properties • Carbon will form _______with other atoms in order to complete its ________shell • The simplest organic chemicals are hydrocarbons

40. Organic Chemistry Primer Methane – a carbon atom bonded to 4 hydrogen Ethane – a carbon-carbon bond Hexane – a 6-carbon chain Isohexane – a branched-carbon chain Cyclohexane – a ringed hydrocarbon

41. Organic Chemistry Primer Double bonding Triple bonding Single bonding There appears to be almost no limit to the number of different structures that carbon can form.  To add to the complexity of organic chemistry, neighboring carbon atoms can form double and triple bonds in addition to single carbon-carbon bonds:

42. Organic Chemistry Primer The Alkanes CnH2n+2

43. Organic Chemistry Primer • A few facts on alkanes • Alkanes are flammable, which is why they are good fuels • Methane is a principle component of natural gas • Butane is a common lighter fluid • They react with oxygen to produce carbon dioxide and water (vapor) The combustion of methane

44. Organic Chemistry Primer • Alkenes • Molecules that contain at least one double-bonded carbon pair • Follow the same naming convention used for alkanes, replacing the prefix –ane with –ene • Follows the expression _________ Ethene

45. Organic Chemistry Primer • Alkynes • Third class of simple hydrocarbons • Contain at least one triple bonded carbon pair • Follow the same naming convention used for alkanes, replacing the prefix –ane with –yne • Follows the expression _________ Ethyne

46. Organic Chemistry Primer • Functional groups • Attach to the hydrocarbons to form additional organic molecules • R stand for the rest of the molecules

47. Organic Chemistry Primer

48. Inorganic Chemistry • This is matter that does not contain carbon • Water • Salts • Acids • Base • A few facts on how this relates to the chemical composition of our bodies • Water is the single most abundant compound in the body • As a universal solvent, it moves nutrients through the body • Water is responsible for chemical reactions and lubrication • Salts are involved in nerve transmission, muscle contractions, blood clotting, metabolism and other reactions

49. Quick Quiz • What is the chemical formula for • Propane • Pentene • Octyne • Methanol • Which of the following statement(s) are true • Water has a low surface tension, allowing it to move through plant roots • Water is mostly found in ice formations • Water molecules are the only substance on Earth that exist in all three physical states of matter: solid, liquid, and gas

50. Quick Quiz • Which of the following statement(s) are true • Water has a low surface tension, allowing it to move through plant roots • Water is mostly found in ice formations • Water molecules are the only substance on Earth that exist in all three physical states of matter: solid, liquid, and gas