CEE 210 ENVIRONMENTAL BIOLOGY FOR ENGINEERS Lecture 1: Biochemistry Basics Instructor: L.R....

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


for Engineers

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


for Engineers

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


for Engineers

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)


for Engineers

Basic Atom

________ (negative)

Nucleus

______ (positive)

_____________ (neutral)


for Engineers

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


for Engineers

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.


for Engineers

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


for Engineers

Periodic Table

26

Fe55.85

Symbol/name

Atomic number-number of electrons-number of protons

Atomic Mass - in amu (atomic mass units)


for Engineers

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.


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.

There are some exceptions to the order when you look at the transition elements, but you get the general idea.


for Engineers

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)


for Engineers

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


for Engineers

Example of Covalent Bond: Methane, CH4

6p6n

1p1n

6p6n

1 p 1 n

1p1n

1p1n

1p1n


for Engineers

Example of Covalent Bond: Methane

C

H

H

HH

C

C


for Engineers

Example of a Double Covalent Bond: Oxygen


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?◦ Two molecules share electrons in their outer orbitals◦ Hydrogen must be present◦ Carbon must be present◦ The bond is highly unstable


for Engineers

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


for Engineers

Ionic Bonding

11p

11n

17p

17n

Na Cl

Na+ Cl-


for Engineers

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


for Engineers

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


for Engineers

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.

- +


for Engineers

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

+- -


for Engineers

Hydrogen Bonding of Water Molecules


for Engineers

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-)

-+

+


for Engineers

Water: The Major Biological Solvent


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


for Engineers

Example of adding an acid or a base Hydrochloric acid dissolves in water

Sodium hydroxide dissolves in water

ClHHCl

OHNaNaOH


for Engineers

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

http://www.visionlearning.com/


for Engineers

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


for Engineers

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


for Engineers

Acid-Base Reactions

HA

A

HA

ApKpH

pHHH

HA

A

KH

HA

AHK

apKpH

a

a

a

10

log

log1

log

11


for Engineers

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


for Engineers

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.


for Engineers

Water – Surface Tension


for Engineers

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) _________


for Engineers

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.


for Engineers

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


for Engineers

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


for Engineers


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:


for Engineers


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


for Engineers

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


for Engineers

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


for Engineers

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


for Engineers

Organic Chemistry PrimerFunctional groups

◦Attach to the hydrocarbons to form additional organic molecules

◦R stand for the rest of the molecules


for Engineers



for Engineers

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


for Engineers

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


for Engineers

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


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


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

Human Anatomy and Physiology, Basic Lessons, by Dr. James Grass◦ http://lrn.org/Content/Lessons/Lessons.html

http://www.biology.arizona.edu/DEFAULT.HTML

http://www.chemguide.co.uk/atoms/properties/atomorbs.html

http://www.physicalgeography.net/fundamentals/8a.html

http://www.chem1.com/acad/sci/aboutwater.html


http://www.biology-online.org/9/1_chemical_composition.htm

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.html

http://lrn.org/Content/Lessons/Lessons.html


for Engineers

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/

http://www.healthnak.com/mind/

http://martingallerycharleston.com/index.html

http://medphoto.wellcome.ac.uk/

http://www.che.wsu.edu/~suha/research/MRI.htm

http://www.adroitsolar.com/natural-gas-pollution/

http://mrbarlow.files.wordpress.com/2009/01/methane-3d-balls.png

http://www.ocf.berkeley.edu/~reetaban/old%20webpage%20folder/

http://www.wildlightgalleries.com/

http://faculty.vassar.edu/suter/1websites/hydrophobicity/images.htm



for Engineers

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

CEE 210 ENVIRONMENTAL BIOLOGY FOR ENGINEERS Lecture 1: Biochemistry Basics Instructor: L.R....

Documents

Transcript of CEE 210 ENVIRONMENTAL BIOLOGY FOR ENGINEERS Lecture 1: Biochemistry Basics Instructor: L.R....