CEE 210 ENVIRONMENTAL BIOLOGY FOR ENGINEERS Lecture 1: Biochemistry Basics Instructor: L.R. Chevalier Department of Civil and Environmental Engineering Southern Illinois University Carbondale
CEE 210 ENVIRONMENTAL BIOLOGY FOR ENGINEERS
Lecture 1: Biochemistry Basics
Instructor: L.R. ChevalierDepartment of Civil and Environmental EngineeringSouthern Illinois University Carbondale
Environmental Biology
for Engineers
ObjectivesReview basic chemistry of small moleculesReview the basic atomUnderstand the orbital structure of the atomReview how a periodic table is organizedUnderstand covalent, ionic and hydrogen
bondingReview the definition of pHSurvey the properties of waterReview major concepts in organic chemistry
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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
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Basic Chemistry of Small MoleculesNames 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)
Oxyge
n
Carbo
n
Hydro
gen
Nitrog
en
Silic
on
Alum
inum Iro
n
Calcium
0
10
20
30
40
50
60
70
80
90
Earth Crust
Humans
Air
% T
ota
l
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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
Fe55.85
Symbol/name
Atomic number-number of electrons-number of protons
Atomic Mass - in amu (atomic mass units)
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Basic Atom
________ (negative)
Nucleus
______ (positive)
_____________ (neutral)
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The ElectronElectrons determine chemical properties of
elements Electrons are outside the nucleusChemical reactions involve sharing or
exchanging electronsElectrons move about the nucleus in atomic
orbitalsThe atom is stable when the outermost
energy level of most atoms has eight electrons
Stability can be achieved by adding, losing, or sharing electrons
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Orbital Structure
6p6n
8p8n
Carbon (Atomic Number 6) Oxygen (Atomic Number 8)
En
erg
y
1s
2s
2p
3s3p
4s4p
3d
Hund’s Law (not to scale)2n2 electrons fill each orbit (n is the # before the letter)Note that 4s has lower energy than 3dThis orbit fills first.
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Orbital Structure
6p6n
8p8n
Carbon (Atomic Number 6) Oxygen (Atomic Number 8)
Energ
y
1s
2s2p
3s3p
4s4p
3d
1s 2s 2p 3s 3p 1s 2s 2p 3s 3p
Also represented as
1s22s22p2
1s22s22p4
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Periodic Table
26
Fe55.85
Symbol/name
Atomic number-number of electrons-number of protons
Atomic Mass - in amu (atomic mass units)
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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.
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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.
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Covalent Bonding:Biologically important chemicals
Element
# of Covalent Bonds
Atomic #
H 1
O 8
N 7
C 6
S 16
P 15
7p7n
Nitrogen (Atomic Number 7)
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Covalent Bond of ChemicalsSharing electrons leads to the formation of
covalent bondsBonds contain energy, and a require energy
to be brokenBond energy (expressed as kcal/mole) is the
energy required to break a bondFor example, an H-H bond requires 104
kcal/mole to break
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Example of Covalent Bond: Methane, CH4
6p6n
1p1n
6p6n
1 p 1 n
1p1n
1p1n
1p1n
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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
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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
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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
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Covalent Bonding of Water
8p8n
1p1n
1p1n
H2O
These three nuclei and 10 electrons possess properties that make it the most unique of more than 15 million chemicals we presently know
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Polarity of Water
8p8n
1 p 1 n
1p1n
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.
- +
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Hydrogen Bonding of Water MoleculesAs 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 H+
-
O
HH
+-O
HH
+- -
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Water: The Major Biological SolventWater dissolves compounds by separating
them into their individual compoundsConsider the illustration below
◦ Sodium chloride (NaCl) is shown in its crystalline form (left)
◦ Then dissolved in water (right)
--
-
-
-
++
++
+
+
+
-
-
-+
+- ++
-+ +
-+
+
- ++
-+
+
-+
+
-
+ Sodium (Na+)
Chlorine (Cl-)
-+
+
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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
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Example of adding an acid or a base Hydrochloric acid dissolves in water
Sodium hydroxide dissolves in water
ClHHCl
OHNaNaOH
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Examples of pH valuespH [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 HydroxideSource http://www.visionlearning.com Library>Chemistry>Acid and Bases
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Acid-Base ReactionsGoverning 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
HA
AHKa
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Acid-Base ReactionsJust 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
HA
AHKa
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Acid-Base Reactions
HA
A
HA
ApKpH
pHHH
HA
A
KH
HA
AHK
apKpH
a
a
a
10
log
log1
log
11
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Water – Unique PropertiesWater 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
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Water – Unique PropertiesWater 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 planetWater 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.
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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.
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) _________
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Carbon - The essential element
6p6n
Carbon (Atomic Number 6)
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.
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Organic Chemistry PrimerOrganic molecules contain both carbon and
hydrogen◦ May contain other elements◦ However the carbon-hydrogen bond defines them
as organicsOrganic chemistry defines life
◦ Millions of different types of living organisms◦ Million of different organic molecules with unique
propertiesCarbon will form _______with other atoms in
order to complete its ________shellThe simplest organic chemicals are
hydrocarbons
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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
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Organic Chemistry Primer
Single bonding
Double 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:
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Organic Chemistry Primer
CarbonAtoms Prefix Alkane
NameChemicalFormula
StructuralFormula
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
The Alkanes CnH2n+2
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Organic Chemistry PrimerA 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)
OHCOOCH 2224 22
The combustion of methane
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Organic Chemistry PrimerAlkenes
◦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
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Organic Chemistry PrimerAlkynes
◦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
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Organic Chemistry PrimerFunctional groups
◦Attach to the hydrocarbons to form additional organic molecules
◦R stand for the rest of the molecules
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Inorganic ChemistryThis 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
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Quick QuizWhat 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
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Quick QuizWhich 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
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ObjectivesReview basic chemistry of small moleculesReview the basic atomUnderstand the orbital structure of the atomReview how a periodic table is organizedUnderstand covalent, ionic and hydrogen
bondingReview the definition of pHSurvey the properties of waterReview major concepts in organic chemistry
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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
Human Anatomy and Physiology, Basic Lessons, by Dr. James Grass◦ http://lrn.org/Content/Lessons/Lessons.html
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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/
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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