CEE 210 Environmental Biology for Engineers
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Lecture 1: Biochemistry Basics CEE 210 ENVIRONMENTAL BIOLOGY FOR ENGINEERS Instructor: L.R. Chevalier Department of Civil and Environmental Engineering Southern Illinois University Carbondale 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 Environmental Biology for Engineers Example of Biochemistry Environmental Biology for Engineers 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 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) 90 80 70 60 % Total 50 40 30 20 10 0 Environmental Biology for Engineers Earth Crust Humans Air 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. 26 Environmental Biology for Engineers Symbol/name Fe 55.85 Atomic number -number of electrons -number of protons Atomic Mass - in amu (atomic mass units) Basic Atom ______ (positive) Nucleus ________ (negative) Environmental Biology for Engineers _____________ (neutral) 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 Environmental Biology for Engineers Orbital Structure Carbon (Atomic Number 6) Oxygen (Atomic Number 8) 6p 6n 8p 8n 3d Energy 3s 2p 2s Environmental Biology for Engineers 1s 4s 4p 3p 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. Orbital Structure Carbon (Atomic Number 6) Oxygen (Atomic Number 8) 6p 6n 1s 2s 2p 8p 8n 3s 3p 1s 2s 2p 3s Also represented as Environmental Biology for Engineers 1s22s22p4 Energy 1s22s22p2 3s 2p 2s 1s 3p 3p 3d 4s 4p Periodic Table 26 Symbol/name Fe 55.85 Environmental Biology for Engineers Atomic number -number of electrons -number of protons Atomic Mass - in amu (atomic mass units) 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. Environmental Biology for Engineers 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. Environmental Biology for Engineers There are some exceptions to the order when you look at the transition elements, but you get the general idea. Covalent Bonding: Biologically important chemicals Element # of Covalent Bonds Atomic # H 1 O 8 N 7 C 6 S 16 P 15 7p 7n Environmental Biology for Engineers Nitrogen (Atomic Number 7) Covalent Bond of Chemicals Environmental Biology for Engineers 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 Example of Covalent Bond: Methane, CH4 6p 6n 1p 1n 6p 6n 1p 1n 1p 1n Environmental Biology for Engineers Example of Covalent Bond: Methane H H C H H C C Environmental Biology for Engineers Example of a Double Covalent Bond: Oxygen Environmental Biology for Engineers 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? ◦ ◦ ◦ ◦ Environmental Biology for Engineers Two molecules share electrons in their outer orbitals Hydrogen must be present Carbon must be present The bond is highly unstable Ionic Bonding Environmental Biology for Engineers 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 Ionic Bonding Na Cl 11p 11n Na+ Environmental Biology for Engineers 17p 17n Cl- 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 Environmental Biology for Engineers Covalent Bonding of Water 1p 1n 8p 8n H2O 1p 1n These three nuclei and 10 electrons possess properties that make it the most unique of more than 15 million chemicals we presently know Environmental Biology for Engineers Polarity of Water - 8p 8n + H2O The four electrons surrounding the oxygen ten to arrange themselves at one side of the molecule, giving the molecule a positive and negative end. Environmental Biology for Engineers 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 + Environmental Biology for Engineers H H - O + - O - O H H H H + Hydrogen Bonding of Water Molecules Environmental Biology for Engineers 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) - + + - + Environmental Biology for Engineers + + - Chlorine (Cl-) Sodium (Na+) - + + + + + - Water: The Major Biological Solvent Environmental Biology for Engineers 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 Environmental Biology for Engineers Example of adding an acid or a base Hydrochloric acid dissolves in water HCl H Cl Sodium hydroxide dissolves in water NaOH Na OH Environmental Biology for Engineers Examples of pH values Environmental Biology for Engineers pH [H+] Example 0 1 x 100 HCl 1 1 x 101 Stomach acid 2 1 x 102 Lemon juice 3 1 x 103 Vinegar 4 1 x 104 Soda 5 1 x 105 Rainwater 6 1 x 106 Milk 7 1 x 107 Pure Water 8 1 x 108 Egg whites 9 1 x 109 Baking soda 10 1 x 1010 Tums antacid 11 1 x 1011 Ammonia 12 1 x 1012 Calcium Hydroxide (Lime) 13 1 x 1013 Drano 14 1 x 1014 Sodium Hydroxide Source http://www.visionlearning.com Library>Chemistry>Acid and Bases Acid-Base Reactions Governing equation ◦ HA H+ + A where HA is the acid A- is the conjugate base ◦ H A Ka HA where Ka is the acid dissociation constant Note: [ ] designates moles/liter Environmental Biology for Engineers 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 H A Ka Environmental Biology for Engineers HA Acid-Base Reactions H A Ka HA 1 1 A H K a HA A pH pK log 1 log log H pH H a 10 pH pKa Environmental Biology for Engineers A HA HA 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 Environmental Biology for Engineers Water molecules are the only substance on Earth that exist in all three physical states of matter: solid, liquid, and gas 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. Environmental Biology for Engineers Water – Surface Tension Environmental Biology for Engineers Water – Unique Properties Environmental Biology for Engineers Temperature (degrees Celsius) Density (grams per cubic centimeter) 0 (solid) 0.9150 0 (liquid) 0.9999 4 ________ 20 ________ 40 0.9922 60 0.9832 80 0.9718 100 (gas) _________ 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. 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. Environmental Biology for Engineers By linking together of many smaller molecules, carbon is able to form very large polymers (macromolecules) many of which are important to human physiology. 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 Environmental Biology for Engineers Carbon will form _______with other atoms in order to complete its ________shell The simplest organic chemicals are hydrocarbons 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 Environmental Biology for Engineers Cyclohexane – a ringed hydrocarbon Organic Chemistry Primer Double bonding Single bonding Triple 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: Environmental Biology for Engineers Organic Chemistry Primer The Alkanes CnH2n+2 Carbon Atoms Environmental Biology for Engineers Prefix Alkane Name Chemical Formula Structural Formula 1 Meth Methane CH 4 CH4 2 Eth Ethane C2H6 CH3CH3 3 Prop Propane C3H8 CH3CH2CH3 4 But Butane C4H10 CH3CH2CH2CH3 5 Pent Pentane C5H12 CH3CH2CH2CH2CH3 6 Hex Hexane C6H14 ... 7 Hept Heptane C7H16 8 Oct Octane C8H18 9 Non Nonane C9H20 10 Dec Decane C10H22 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) CH4 2O2 CO2 2H 2O The combustion of methane Environmental Biology for Engineers Organic Chemistry Primer Alkenes ◦ Molecules that contain at least one doublebonded carbon pair ◦ Follow the same naming convention used for alkanes, replacing the prefix –ane with –ene ◦ Follows the expression _________ Ethene Environmental Biology for Engineers 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 Environmental Biology for Engineers Organic Chemistry Primer Functional groups ◦ Attach to the hydrocarbons to form additional organic molecules ◦ R stand for the rest of the molecules Environmental Biology for Engineers Organic Chemistry Primer Environmental Biology for Engineers Inorganic Chemistry This is matter that does not contain carbon ◦ ◦ ◦ ◦ A few facts on how this relates to the chemical composition of our bodies ◦ ◦ ◦ ◦ Environmental Biology for Engineers Water Salts Acids Base 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 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 Environmental Biology for Engineers 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 Environmental Biology for Engineers 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 Environmental Biology for Engineers References The Biology Project, University of Arizona ◦ http://www.biology.arizona.edu/DEFAULT.HTML Chemguide ◦ http://www.chemguide.co.uk/atoms/properties/atomorbs.html Water ◦ http://www.physicalgeography.net/fundamentals/8a.html Water and its structure ◦ http://www.chem1.com/acad/sci/aboutwater.html Vision Learning ◦ http://www.visionlearning.com/ Biology Online ◦ http://www.biology-online.org/9/1_chemical_composition.htm On-line Biology Book by Michael J. Farabee ◦ http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.html Environmental Biology for Engineers Human Anatomy and Physiology, Basic Lessons, by Dr. James Grass ◦ http://lrn.org/Content/Lessons/Lessons.html Sources of photographs and images Human brain ◦ http://www.healthnak.com/mind/ X-rays images ◦ http://martingallerycharleston.com/index.html Cold Virus (altered in Photoshop) ◦ http://medphoto.wellcome.ac.uk/ MRI Scan ◦ http://www.che.wsu.edu/~suha/research/MRI.htm Methane ◦ http://www.adroitsolar.com/natural-gas-pollution/ ◦ http://mrbarlow.files.wordpress.com/2009/01/methane-3d-balls.png Water droplet ◦ http://www.ocf.berkeley.edu/~reetaban/old%20webpage%20folder/ ◦ http://www.wildlightgalleries.com/ Water strider ◦ http://faculty.vassar.edu/suter/1websites/hydrophobicity/images.htm Hydrocarbons ◦ http://www.visionlearning.com/ Environmental Biology for Engineers About the Instructor Environmental Biology for Engineers Professor, Civil and Environmental Engineering, Southern Illinois University Carbondale Fellow, American Society of Civil Engineers (ASCE) Diplomat, Water Resources Engineering, American Academy of Water Resources Engineering (AAWRE) Board Certified Environmental Engineer, American Academy of Environmental Engineers (AAEE) Licensed Professional Engineer, State of Illinois
