1. CEE 210 Environmental Biology for Engineers
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 Fe 26 55.85 Element Atom Proton Neutron Electron Isotope
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 Fe
55.85
Symbol/name
Atomic number
number of electrons
number of protons
Atomic Mass
- in amu (atomic mass units)

6. Basic Atom ______ (positive) ________ (negative)
Nucleus
______ (positive)
_____________ (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 1s 2s 2p 3s 3p 1s 2s 2p 3s 3p
Energy 1s 2s 2p 3s 3p 4s 4p 3d
Also represented as
1s22s22p2
1s22s22p4

10. Periodic Table Fe 26 55.85 Atomic number number of electrons
Symbol/name
Atomic number
number of electrons
number of protons
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
Element
# of Covalent Bonds
Atomic # H 1 O 8 N 7 C 6 S 16 P 15 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

16. Example of Covalent Bond: Methane

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
17p
17n Na Cl
11p
11n
Cl-
Na+

21. Water 70% of the Earth's surface is covered with this simple molecule
Scientists estimate that the hydrosphere contains about 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 Water1p 1n
H2O 8p 8n 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

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

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 O H + - O H + -

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
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 pH [H+] Example 1 x 100 HCl 1 1 x 101
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 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 ° 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
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.

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
Carbon Atoms
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

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

51. 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

52. References The Biology Project, University of Arizona Chemguide Water
Chemguide
Water
Water and its structure
Vision Learning
Biology Online
On-line Biology Book by Michael J. Farabee
Human Anatomy and Physiology, Basic Lessons, by Dr. James Grass

53. Sources of photographs and images
Human brain
X-rays images
Cold Virus (altered in Photoshop)
MRI Scan
Methane
Water droplet
Water strider
Hydrocarbons

54. About the Instructor
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