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Final Exam 40%

Exams 45%

Report 5%

Homework 10%

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Organic Compounds

Proteins

Carbohydrates

Lipids

Nucleic Acids

Cell structure

Metabolism Molecular Genetics

Recombinant DNA

Genomics

Proteomics

Bioreactors

Other applications

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Organic Chemistry

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Refinery and tank storage facilities, like this one inTexas, are needed to change the hydrocarbons ofcrude oil to many different petroleum products. Theclasses and properties of hydrocarbons form one

topic of study in organic chemistry.

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Organic Compounds

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An organic compound is one that has carbonas the principal element

An inorganic element is any compound that isnot an organic compound.

Carbon is unique

› It has 6 electrons in its outer shell arranges 1s2

2s2

sp2

 › It has room for 4 bonds to 4 other atoms.

Organic compounds have specific geometryaround the carbon to carbon bond.› If there are four atoms or groups around a carbon

atom, it has a tetrahedral geometry.

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(A)The carbon atomforms bonds in atetrahedral structure

with a bond angle of109.5O. (B) Carbon-to-carbon bond angles are109.5O, so a chain of

carbon atoms makes azigzag pattern. (C) Theunbranched chain ofcarbon atoms is usually

simplified in a way thatlooks like a straightchain, but it is actually azigzag, as shown in (B).

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Hydrocarbons

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Introduction

› A hydrocarbon is a compound consisting of onlyhydrogen and carbon.

› The carbon to carbon can be single, double, or triple bonds.

› The bonds are always nonpolar.› Alkanes are hydrocarbons with only single bonds.

Alkanes occur in what is called a homologous series.

Each successive compound differs from the one

before it only by a CH2

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Carbon-to-carbon bondscan be single (A), double(B), or triple (C). Note that

in each example, eachcarbon atom has four dashes, which representfour bonding pairs of

electrons, satisfying theoctet rule.

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Carbon-to-carbon chainscan be (A) straight, (B)

branched, or (C) in a closedring. (Some carbon bondsare drawn longer, but areactually the same length.)

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› Compounds that have the same molecular formula, but different structures (arrangements ofthe atoms) are called isomers.

› Naming alkanes 

Identify the longest continuous chain.

The locations or other groups of atomsattached to the longest chain are identifiedand numbered by counting from the end ofthe molecule which keeps the numberingsystem as low as possible.

Hydrocarbon groups that are attached to

the longest continuous chain and namedusing the parent name and changing the – ane suffix to – yl.

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Recall that amolecular formula(A) describes the

numbers of differentkinds of atoms in amolecule, and astructural formula

(B) represents a two-dimensional modelof how the atomsare bonded to

each other. Eachdash represents abonding pair ofelectrons.

(A)A t i ht h i

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(A)A straight-chainalkane is identifiedby the prefix n- for "normal" in the

common namingsystem. (B) Abranched-chainalkane isomer isidentified by the

prefix iso- for "isomer" in thecommon namingsystem. In theIUPAC name,isobutane is 2-methylpropane.(Carbon bonds areactually the same

length.)

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Alkenes and Alkynes

› Alkenes are hydrocarbons with at least onedouble carbon to carbon bond.

To show the presence of the double bond,

the – ane suffix from the alkane name is

changed to – ene.› The alkenes are unsaturated with respect to

hydrogen

This means it does not have the maximum

number of hydrogen atoms as it would if it

were an alkane (a saturated hydrocarbon).

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Ethylene is the gas that ripens fruit, and a ripe

fruit emits the gas, which will act on unripe fruit.

Thus, a ripe tomato placed in a sealed bag with

green tomatoes will help ripen them.

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› Naming is similar to naming alkanes except:

The longest continuous chain must contain

the double bond. The base name now ends in – ene.

The carbons are numbered so as to keep thenumber for the double bond as low aspossible.

The base name is given a number whichidentifies the location of the double bond.

An alkyne is a hydrocarbon with at least onecarbon to carbon triple bond.

› Naming an alkyne is similar to the alkenes, exceptthe base name ends in – yne.

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Cycloalkanes and Aromatic Hydrocarbons

› Cycloalkanes are alkanes (only carbon to carbonsingle bonds) which form a ring structure.

› An aromatic compound is one that is based onthe benzene ring.

A benzene ring that is attached to another compound is given the name phenyl.

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(A)The "straight" chainhas carbon atoms that

are able to rotate freelyaround their singlebonds, sometimes linkingup in a closed ring. (B)Ring compounds of thefirst four cycloalkanes.

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(A)The bonds in C6H6 are something

between single anddouble, which gives itdifferent chemicalproperties thandouble-bondedhydrocarbons. (B) Thesix-sided symbol with acircle represents thebenzene ring. Organic

compounds based onthe benzene ring arecalled aromatichydrocarbonsbecause of their aromatic character.

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Petroleum

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Petroleum is a mixture of alkanes,cycloalkanes, and aromatic hydrocarbons.

› Petroleum is formed from the slow decompositionof buried marine life, primarily plankton and algae.

As petroleum is formed it is forced through

porous rock until it reaches an imperviouslayer of rock.

› Here it forms an accumulation of petroleum andsaturated the porous rock creating an oil field.

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Petroleum was once used for medicinalpurposes.

› It was first distilled by running through a whiskeystill, in an attempt to make it taste better.

› The liquid that he obtained burned quite well in

lamps.› This clear liquid that was obtained from petroleum

distillation was called kerosene.

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Crude oil is the petroleum that is pumpeddirectly from the ground.

› It is a complex mixture of hydrocarbons with oneor two carbon atoms up to a limit of about 50

carbon atoms.› This is usually not useful, so it must separated by

distillation.

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Crude oil from the ground is separated into usablegroups of hydrocarbons at this Louisiana refinery.Each petroleum product has a boiling point range,or "cut," of distilled vapors that collect in condensingtowers.

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Petroleumproductsand theranges ofhydrocarbo

ns in eachproduct.

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The octanerating scale is a

description ofhow rapidlygasoline burns.It is based on(A) n-heptane,with anassignedoctane number of 0, and (B)

2,2,4-trimethylpentane, with anassignednumber of 100.

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Hydrocarbon Derivatives

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Introduction

› Hydrocarbon derivatives are formed when one or more hydrogen atoms is replaced by an elementor a group of elements other than hydrogen.

› Halogens (F2, Cl2, Br 2, I2,) can all add to ahydrocarbon to form am alkyl halide.

When naming the halogen the – ine ending isreplaced by – o

Fluorine becomes fluoro

Chlorine becomes chloro

Bromine becomes bromo

Iodine becomes iodo

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Common examples of organic halides.

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› Alkenes can also add to each other in an addition

reaction to form long chains of carboncompounds.

this is called polymerization

The atom or group of atoms that are added to thehydrocarbon are called functional groups.

Functional groups usually have multiple

bonds or lone pairs of electrons that make

them very reactive.

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Alcohols› An alcohol has a hydrogen replaced by a

hydroxyl (-OH) group.› The name of the hydrocarbon that was substituted

determines the name of the alcohol.› The alcohol is named using the hydrocarbon

name and adding the suffix – ol.

If methane is substituted with an OH group itbecomes methanol

If a pentane group is substituted with an OHgroup it is pentanol.

For alcohols with more than two carbonatoms we need the number the chain so asto keep the alcohol group as low as possible.

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Four different alcohols. TheIUPAC name is given above

each structural formula, andthe common name is givenbelow.

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Gasoline is a mixture of hydrocarbons (C8H18 for example) that contain no atoms of oxygen. Gasoholcontains ethyl alcohol, C2H5OH, which does containoxygen. The addition of alcohol to gasoline,therefore, adds oxygen to the fuel. Since carbon

monoxide forms when there is an insufficient supplyof oxygen, the addition of alcohol to gasoline helpscut down on carbon monoxide emissions. Anatmospheric inversion, with increased air pollution, islikely during the dates shown on the pump, so that iswhen the ethanol is added.

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› The OH group is polar and short chain alcohols are

soluble in both nonpolar alkanes and water.› If an alcohol contains two OH groups it is a diol

(sometimes called a glycol).

› An alcohol with three OH groups is called a triol (sometimes called a glycerol).

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Commonexamples of

alcohols withone, two, andthree hydroxylgroups per molecule. TheIUPAC name isgiven aboveeach structuralformula, andthe commonname is givenbelow.

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Ethers, Aldehydes, and Ketones

› An ether has a general formula ROR’ 

Diethyl ether for example would have the formulaCH3CH2OCH2CH3 

› An aldehyde has a carbonyl group (carbondouble bonded to an oxygen) attached to aterminal carbon atom

› A ketone has a carbonyl group attached to aninternal carbon atom.

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The carbonyl group (A)is present in bothaldehydes andketones, as shown in(B). (C) The simplest

example of each, withthe IUPAC nameabove and thecommon name beloweach formula.

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Organic Acids and Esters› Organic acids are those acids that are derived

from living organisms, usually from metabolism, butsometimes as a defense mechanism.

› Long chain organic acids are known as fattyacids.

› These are also called carboxylic acids as theycontain the carboxyl functional group (COOH)

One oxygen is double bonded to the carbon andthe other is bonded to the carbon and to thehydrogen both with single bonds.

› Esters are condensation products of carboxylicacids with the removal of water (also called adehydration synthesis).

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These red ants, like other ants, make the simplest ofthe organic acids, formic acid. The sting of bees,ants, and some plants contains formic acid, alongwith some other irritating materials. Formic acid isHCOOH.

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Organic Compounds of Life

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Introduction

› Living organisms have to be able to:

Exchange matter and energy with their 

surroundings.

Transform matter and energy into differentforms.

Respond to changes in their environment.

Grow. Reproduce.

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› All of these changes are due to large organic

compounds called macromolecules. A macromolecule is a combination of many smaller 

similar molecules polymerized into a chain structure.

› In living organisms there are three main types of

macromolecules which control all activities anddetermine what an organism will do and become.

Proteins.

Carbohydrates

Nucleic acids.

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› The basic unit of life is the cell.

The cell makes up all living organisms that we know

of. Cells are in turn made of macromolecules that form

inside the cell.

Other macromolecules control the formation of

these macromolecules.› Metabolism is the breaking down or building up of

macromolecules.

Generally, breaking down macromolecules releases

energy that the organism can use as an energysource.

The building up of macromolecules requires energy,that is obtained from breaking down

macromolecules.

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Proteins

› Proteins are macromolecules that are polymers of

amino acids.

› Structurally, proteins go into making muscle tissue,connective tissue, and skin, hair, and nails, just toname a few.

› Functionally proteins are enzymes which catalyzebiochemical reactions

Building up macromolecules requires energy and an

enzyme lowers the amount of energy that isnecessary.

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› There are 20 amino acids that go into producing

proteins.

These amino acids are polymerized by a

dehydration synthesis to form long chains of

repeating amino acids called a protein. The arrangement of the amino acids in the

polymer determine the structure of the

protein which confers to it is function or 

structural attributes.

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The twenty aminoacids that make

up proteins, withthree-letter abbreviations. Thecarboxyl group of

one amino acidbonds with theamino group of asecond acid toyield a dipeptideand water.Proteins arepolypeptides.

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Part of a protein polypeptide made up of theamino acids cysteine (cys), valine (val), andlysine (lys). A protein can have from fifty to onethousand of these amino acid units; each protein

has its own unique sequence.

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Carbohydrates

› Carbohydrates are a large group of compoundsthat are generally called sugars, starches, andcellulose (all of which are sugars or polymers ofsugars)

› Generally sugars are a storage source of energy.

By breaking sugars down into carbon dioxide andwater, living organisms can release the energy that islocked up in them to use for energy requirements.

› Glucose is the carbohydrate that animals utilizemostly for their energy.

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Glucose (blood sugar) is an aldehyde, andfructose (fruit sugar) is a ketone. Both have a

molecular formula of C6H12O6

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› Classification

A monosaccharide is one that is made up of

 just one sugar unit.

A disaccharide is one that is made up of two

sugar units. A polysaccharide is one that is made up of

many sugar units.

These plants and their

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These plants and their flowers are made up of amixture of carbohydratesthat were manufactured

from carbon dioxide andwater, with the energy ofsunlight. The simplest of thecarbohydrates are themonosaccharides, simple

sugars (fruit sugar) that theplant synthesizes. Food isstored as starches, whichare polysaccharides madefrom the simpler 

monosaccharides. Theplant structure is heldupright by fibers of cellulose,another form of apolysaccharide.

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› Starch is a storage carbohydrate used by plants.

When plants photosynthesize the use theenergy from sunlight to convert carbon

dioxide and water into sugars and oxygen.

› Glycogen is a storage carbohydrate used by

animals.

› Cellulose is a polysaccharide that is used in plantcell walls to maintain their structure.

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Starch and cellulose are both polymers of glucose,but humans cannot digest cellulose. The differencein the bonding arrangement might seem minor, butenzymes must fit a molecule very precisely. Thus,enzymes that break down starch do nothing to

cellulose.

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Fats and Oils › Humans take in amino acids and utilize them to

synthesize the polymers that are called proteins.

There are 10 amino acids which humanscannot synthesize themselves and must be inthe diet, these are called essential aminoacids.

› Humans also take in carbohydrates and use thebreak down of the carbohydrate as an energysource.

› When either of these is taken in in quantities abovethat that is necessary for the body, they areconverted into fats in animals and oils in plants. Fats and oils are a long term storage for 

energy sources.

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› Animal fats are wither saturated or unsaturated,but most are saturated.

Unsaturated fats are believed to lower cholesterol levels in humans.

Saturated fats and cholesterol are thought to

contribute to hardening of the arteries.› Fats are stored in adipose tissue which has an

insulating function, a padding (protective)function, as well as a storage function.

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The triglyceridestructure of fats

and oils. Note theglycerol structureon the left andthe ester structureon the right. Alsonotice that R1,R2, and R3 arelong-chainedmolecules of 12,

14, 16, 18, 20, 22,or 24 carbonsthat might besaturated or unsaturated.

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Synthetic Polymers

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Polymers

› Polymers are long molecules with repeating

structures of simpler molecules.

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Syntheticpolymers,thepolymer unit, and

someuses ofeachpolymer.

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Petroleum andcoal as sources of

raw materials for manufacturingsyntheticpolymers.

S f I t t F ili f

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Chapter 2 62

Summary of Important Families ofOrganic Compounds

Summary (cont )

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Chapter 2 63

Summary (cont.)

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Infrared Spectroscopy: An InstrumentalMethod for Detecting Functional Groups

› Electromagnetic radiation in the infrared (IR)frequency range is absorbed by a moleculeat certain characteristic frequencies

Energy is absorbed by the bonds in the molecule

and they vibrate faster 

The bonds behave like tiny springs connectingthe atoms

The bonds can absorb energy and vibrate

faster only when the added energy is of aparticular resonant frequency

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Chapter 2 65

The frequencies of absorption are verycharacteristic of the type of bonds containedin the sample molecule

The type of bonds present are directly relatedto the functional groups present

A plot of these absorbed frequencies iscalled an IR spectrum

› Infrared Spectrometer 

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Chapter 2 66

p

An infrared spectrometer detects thefrequencies absorbed by the sample

molecule Light of all the various IR frequencies is

transmitted to the molecule and thefrequencies absorbed are recorded

The absorption frequencies are specified aswavenumbers in units of reciprocalcentimeters (cm-1)

Alternatively the wavelength (l) in units of microns(mm) can be specified

The spectrum is a plot of frequency on thehorizontal axis versus strength of absorption

on the vertical axis

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Chapter 2 67

There are different types of stretching andbending vibrations induced by theabsorption of infrared energy

The actual relative frequency of vibrationcan be predicted

Bonds with lighter atoms vibrate faster than those

with heavier atoms

Triple bonds (which are stiffer and stronger)

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Chapter 2 68

Triple bonds (which are stiffer and stronger)vibrate at higher frequencies than doublebonds

Double bonds in turn vibrate at higher frequenciesthan single bonds

The IR spectrum of a molecule usuallycontains many peaks These peaks are due to the various types of

vibrations available to each of the different bonds Additional peaks result from overtone (harmonic)

peaks which are weaker and of lower frequency

The IR is a “fingerprint” of the molecule becauseof the unique and large number of peaks seen for a particular molecule

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Chapter 2 69

IR Spectra

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Chapter 2 70

only certain peaks are interpreted in

ks that are large and above 1400 cm-1 are

able

ons

retching regions from 2800-3300 cm-1 eristic of the type of carbon theis attached to

s where the carbon has more  s r are shorter, stronger and stiffer and

te at higher frequencys at sp centers appear at 3000-3100 cm-1 

s at sp2 centers appear at about 3080 cm-1 

s at sp3 centers appear at about 2800-3000

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› Example: octane

› Example: 1- hexyne

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› Alkenes

The C-H bending vibration peaks locatedat 600-1000 cm-1 can be used to determinethe substitution pattern of the double bond

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› Example: 1-hexene

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› Aromatic Compounds

The C-C bond stretching gives a set of

characteristic sharp peaks between 1450-1600 cm -1 

Example: Methyl benzene