Organic Chemistry Chapter 20

What is organic chemistry? The name implies that it is the chemistry of living things That is partially true Organic chemistry- the study of carbon containing compounds (*with a few exceptions-like CO 2 ) All living things are carbon based. However, carbon is not only involved in living things.

Why does carbon get its own class of chemistry? Since carbon can form 4 covalent bonds it has a large number of possibilities for structures. It also readily bonds with other carbon atoms forming chains or rings, which gives it billions of stable structures. Also, living things continuously do “experiments” making new carbon compounds.

…because there are so many useful carbon compounds Chemistry is basically split into organic and inorganic. Carbon chemistry and everything else, and the everything else didn’t really become important until recently. Since living things naturally make all of these carbon compounds, man found several uses for them without having to manufacture them.

Just a small sampling Some carbon compounds include DNA, diamonds, natural gas, aspirin, octane, polyester, freon, asphalt… Caffeine, carbohydrates, plastics, rubber, acrylic, vinyl, graphite, proteins, propane… Vinegar, citric acid, leather, TNT, alcohol, ibuprofen, soot, cellulose, butane etc. There are more known compounds of carbon than there are for all other elements combined!

Allotropes of pure carbon Allotrope- Different molecular structure of molecules containing the same atom Diamonds- dense tetrahedral network Graphite- layers laying on top of each other Buckminsterfullerene or buckyball ~ found in soot ( a sphere)

Simplest organic compounds Hydrocarbons- compounds containing carbon and hydrogen Alkanes- straight chain hydrocarbons with all single bonds Organic molecules follow their own system of nomenclature (naming) Alkanes get the suffix “-ane”

Naming and drawing organic compounds

Root words # of C atoms Meth1Hex6 Eth2Hept7 Prop3Oct8 But4Non9 Pent5Dec10

So for example H-C-C-C-C-H H H H-C-C-C-C-C-C-C-C-H H H H H H-C-C-C-H H H H H H-C-H H butane octane propane methane

Molecular Formulas Alkanes always have the molecular formula of: C x H 2x+2 2 H on every C except the end, they get 3 Hexane- C 6 H 14  molecular formula H-C-C-C-C-C-C-H H H H Lewis Dot, or Structural Formula

Skeleton Formulas Drawing Lewis Dot structural formulas for long organic compounds can get rather tedious. So organic has shortened it They don’t write the C’s or the H’s You draw a jagged line, at each corner there is a Carbon Assume all extra spaces are filled with H

For Example Heptane, C 7 H 16 H-C-C-C-C-C-C-C-H H H H H H H H = Nonane, C 9 H 20 H-C-C-C-C-C-C-C-C-C-H H H H H H H H H H =

Isomers Isomers- compounds with the same molecular formula but different structural formulas Different structural formulas mean it has different properties Butane is the first alkane with a possible isomer H-C-C-C-C-H H H = or H-C- C - C-H H H H H HCH H H Both are C 4 H 10

Naming Isomers Name the longest chain possible. As a prefix, name the chain attached with –yl on the end and give the number of the carbon atom it is attached to Longest Chain heptaneethyl It could also be 5 ethyl heptane if you started numbering from the other side, when given an option always go with the Lower number!!!

Name this molecule 4 ethyl octane And give its molecular formula C 10 H 22 4 propyl decane C 13 H 28

Cyclic Hydrocarbons A hydrocarbon that is a ring instead of a chain. To name it, give it the prefix “cyclo-” Molecular Formula Subtract 2 H from C x H 2x+2 C x H 2X cyclobutane H-C-C-H H C4H8C4H8

Name the following compounds and give their formula cyclohexane C 6 H 12 cycloheptane C 7 H 14 cyclooctane C 8 H 16 cyclodecane C 10 H 20

Name and give the formula Methyl cyclohexane C 7 H 14

Alkenes Contain a double bond They get the suffix “-ene” and the number of the carbon atom the double bond is on (lowest number) Molecular formula Subtract 2 H for each double bond from C x H 2x+2 H-C=C-C-C-H H H H 1 butene Skeleton fomula C4H8C4H8

Alkynes Contain a triple bond They get the suffix “-yne” and the number of the carbon atom the triple bond is on. Molecular formula subtract 4 H for each triple bond from C x H 2x+2 H-C-C=C-C-C-H H H H 2 pentyne Skeleton fomula C5H8C5H8

Name and give the formula for these compounds 2 hexeneC 6 H 12 3 methyl nonaneC 10 H 22 ethyne (commonly known as acetylene) C2H2C2H2 3 methyl 1 pentene C 6 H 12 Cyclopentane C 5 H 10

Name and give the formula for these compounds 2 hepteneC 7 H 14 1 butyne C4H6C4H6 3 ethyl 1 hexene C 8 H 16 Cyclopentene C5H8C5H8 cyclopropane C3H6C3H6

Doubles and triples If you have two of the same thing put “di” in front of it If you have three of the same thing put “tri” in front of it

Examples 2,3 hexadiene 3,4,4 trimethyl heptane C 6 H 10 C 10 H 22

Multiple groups on a chain Name each and put them in alphabetical order 3, 4 diethyl 2 methyl 1 heptene C 12 H 24

Functional Groups Things attached to carbon chains

Functional Groups Atoms other than hydrogen or carbon covalently bonded to a carbon atom in an organic molecule. Most commonly oxygen, nitrogen, or the halogens. The presence of a functional group drastically changes the chemical properties of a molecule.

Different Functional groups with a 2 carbon chain Ethane- gas (found in natural gas) Ethanol- grain alcohol (drinkable) Ethanoic acid- vinegar Diethyl ether- starting fluid Chloro fluoro ethane (CFC’s used as refrigerants) Ethanal- foul smelling liquid (similar to formaldehyde)

Halogenated Hydrocarbons Hydrocarbons with halogens attached Before the main chain name the halogen as either fluoro, chloro, bromo or iodo and give its number For each halogen subtract 1 H Cl 1,3-dichloro cycloctane C 8 H 14 Cl 2

Practice F 2 fluoro 1 butene C4H7FC4H7F Br 2,5-dibromo 3-ethyl 4-methyl heptane C 10 H 20 Br 2

Alcohols Hydrocarbons with an –OH attached To name it, give it the suffix –(an)ol and the number the OH is attached to Normally you subtract one H from the main group and put an OH on the end (to signify it is an alcohol) OH Ethanol C 2 H 5 OH HOHO 2 propanol Commonly Isopropanol or Rubbing alcohol C 3 H 7 OH

Aldehydes Hydrocarbons with a =O on the outer edge of the chain (most have a foul stench, like formaldehyde or methanal) To name it add the suffix “–al” For the formula subtract 2 H and add O O=O= hexanal C 6 H 12 O =O octanal C 8 H 16 O

Ketones Hydrocarbons with a =O not on the edge of the compound To name it add the suffix “–one” For the formula subtract 2 H and add O O= cyclopropanone C3H4OC3H4O O= 3-nonanone C 9 H 18 O

Carboxylic Acid Hydrocarbons with a –COOH group attached To name it give it the suffix “–oic acid”, the C in the group does count Subtract one C one H and add COOH This group looks like… -C=O OHOH =O OHOH Pentanoic acid C 4 H 9 COOH

Everything so far… Alkanes, alkenes, and alkynes Isomers, halogenated and cyclic Alcohols R-OH *R means any carbon chain -ol Carboxylic Acids R-C=O -OH -oic acid Aldehydes R=OR=O -al Ketones R-C-R =O -one on the end

2,4 dichloro 3 methyl 1 cyclobutanone 2, 3 dimethyl hexanoic acid C 5 H 6 Cl 2 O C 7 H 15 COOH

3 bromo 2, 2 diethyl 1 hexanal 2, 2 dibromo 1 cyclohexanol C 10 H 19 BrO C 6 H 9 Br 2 OH

Large Molecule (ATP)

Petroleum Products

What is petroleum? Also known as crude oil It is a thick black sludge It comes from ancient plant and animal life long since buried and kept under extreme pressure for millions of years. It is composed of countless different organic compounds.

What is made from petroleum Gasoline, kerosene, and rocket fuel Most plastics and other polymers (elastomers and fibers) Synthetic rubbers and fabrics Most pharmaceutical drugs And several other things If we run out of petroleum it would have a devastating effect on us

Petroleum is separated in a fractionating tower Fractionating Tower- structure where crude oil is heated to boiling and different structures are collected at different temperatures Fractionating Tower Crude oil in Heat Kerosene condenses Gasoline condenses Natural Gas (doesn’t Condense) Asphalt never vaporizes There are several other things pulled out that I didn’t include.

One compound that comes from petroleum Benzene Which changes to… And back again constantly Double bonds Are a little shorter Than single bonds But in benzene all Bonds are the Same length. It also is drawn as

Compounds that contain benzene are called aromatic Aspirin (acetyl salicylic acid) O= O-H O O

Compounds that contain benzene are called aromatic Trinitro Toluene (TNT) O 2 N-- NO 2 O 2 N-

A few other aromatics Vinyl, napthalene (found in moth balls), acetaminophen, penacillin Benzene is an extremely common organic compound The fact that the double bonds flip back and forth (called resonance) give it a very stable structure

IUPAC vs. Common and copyrighted names Several compounds have names similar to what we went over but slightly different. Common names for several compounds have been around for centuries and are still used (acetic acid, formaldehyde) Several other names were copyrighted for sale (acetaminophen and polypropylene)

To burn or to build? Burning hydrocarbons normally produces carbon dioxide. As our fossil fuels use has increased, so have our CO 2 levels. Petroleum products are used to produce several fuel sources as well as polymers.

Polymerization

A functional group we did not cover… Esters- a functional group in the middle of a carbon chain; R-COO-R It gets the suffix –oate (you won’t have to name these!) R-C-O-R O= It is very similar to carboxylic acids R-C-O-H O= ~In fact it is formed by a carboxylic acid and an alcohol H-O-R + R-C-O-R O= + H-O-H the water came from…

Now if you have a few compounds that have both a Carboxylic acid end R-C-O-H O= +an alcohol end H-O-R-C-O-H O= H-O- + They could form an ester that looks like… + H-O-H R-C-O- O= H-O-R-C-O-H O= But the compound still has a… Carboxylic acid end And an alcohol end So it could repeat this process thousands even millions of times and make a whole bunch of… esters Of course the scientific prefix for “whole bunch of” is poly

This is the basis for a polymer Polymer-A large chain-like molecule composed of smaller molecules linked together The smaller units it is made up of are called monomers monomers need to have ends that can join together (or stack on top of one another) Like an extension cord or markers So you could (infinitely) join them together to make a large polymer

Polymers can get very large common polymers have a molecular mass of around 50,000 g/mol The first molecules seen under a microscope were polymer chains Common polymers include things like… Nylon, Kevlar©, latex, PVC, rubber, acrylic, vinyl, Deoxyribonucleic acid (DNA) and carbohydrates

Piece of DNA

Polymers are put into three classes Elastomers- Polymers that can be stretched to 10x their normal size and return to their original shape Fibers Polymers that cannot stretch or be reshaped once formed Plastics Polymers that can stretch and flex more than fibers but less than elastomers Elastic Nylon and Acrylic Polypropylene polystyrene and PVC (polyvinyl chloride)

Biochemistry Chapter 21

Elements in the body About 96% of the mass of the human body is made up of 4 elements Oxygen 65% carbon 18% hydrogen 10% nitrogen 3% The only other elements that make up a significant portion are: Calcium 1.5% Phosphorus 1.2%

Water Of course, the vast majority of the oxygen is found in water. Water is essential for life. It is what all chemical reactions in the body occur in. However, water is not considered a biochemical or organic compound. Organisms are not bonded to water, instead water is contained within the organism.

If we remove water… Then the human body is made up of 37% carbon 30% oxygen 18% hydrogen 6.2% nitrogen 3.1% calcium 2.5% Phosphorus

Elements Essential to Life The green elements are called “trace” elements because they make up less than.05%.

Uses of elements Carbon is a requirement for all biochemical compounds Nitrogen is needed for proteins Iron is needed for using oxygen t.html t.html

Biochemical Compounds These elements are bonded together to form different biochemical compounds. Biochemical compounds include: Proteins Carbohydrates Nucleic acids Lipids

Proteins Proteins are polymers made up of monomers called amino acids. Amino acids have a carboxylic acid end and an amine (NH 2 ) end. Bonding an amine group and carboxylic acid is called a peptide bond.

Amino acid to protein H-N-R-C-O-H O= H- Carboxylic Acid Amine Group + H-N-R-C-O-H O= H- H-N-R-C- H- + H-O-H N-R-C-O-H H- O= Peptide bond This has to repeat at least 50x for it to be a protein Otherwise it is just a polypeptide. Amino acid R is any carbon chain Protein

Amino acids

Proteins A protein is at least 50 amino acids linked together. This makes proteins very large molecules. Most have a molar mass between ,000,000 g/mol.

Protein Structure Proteins naturally fold into distinct 3-D structures. It is based off of a few different aspects. Primary structure of proteins is the amino acid sequence. 3 letter or one letter abbreviations are used for each amino acid. gly-cys-met-asp- Glycine-cytoseine-methionine-aspartic acid-

Secondary structures The secondary structure is local structures formed throughout the molecule. Alpha helix, beta pleated sheet, and turns are common formations. Alpha helix is when the molecules start to spiral around. Beta pleated sheet is when the molecules take a jagged back and forth formation. Turns are when the chain flips directions.

Triose Phosphate Isomerase Alpha helix Beta pleated sheet Turns

Tertiary Structure of proteins Tertiary structure- the overall structure of the protein. This greatly effects the function of the protein. Enzymes are proteins that catalyze certain reactions. Enzymes work at specific spots on an molecule.

Other functions of proteins Structure- Tendons, bones, skin, cartilage, hair, are mainly protein Movement- Muscles are mainly protein Transport- hemoglobin, a protein, carries oxygen to cells from the lungs Protection- antibodies that fight off foreign substances are proteins Control- many hormones such as insulin are proteins.

Carbohydrates Carbohydrates are second class of biochemical compounds. They are commonly polymers made up of monomer units called simple sugars or monosaccharides. Simple sugars are ketones or aldehydes with several –OH (hydroxyl) groups attached.

D Glucose

Bonding These sugars normally bend around to form rings. Then they link together. Two sugars bonded together are called a disaccharide. Sucrose (common table sugar) is a disaccharide of glucose and fructose.

Sucrose

Polysaccharides Polysaccharides are large molecules made of many simple sugars. Starch is the main fuel reservoir in plants. Cellulose is the main structural component for plants. Both are polysaccharides, but because of different types of bonds, humans are only capable of digesting starch not cellulose.

Glycogen Animals, and humans, store carbohydrates as glycogen. These are large polysaccharide molecules that are broken down into simple sugars as you need them.

Carbohydrates Uses In animals, carbohydrates are used as fuel sources. Plants uses carbohydrates as both a fuel source and structural support.

Nucleic Acids The biochemical polymer that stores and transmits genetic information in a cell is a polymer called deoxyribonucleic acid, DNA. DNA carries the instructions for making a specific protein. Ribonucleic Acid, RNA is needed to translate and copy DNA.

Nucleic acids Nucleic acids are polymers made up of nucleotides. A nucleotide consists of a nitrogen containing base, a 5 carbon sugar, and a phosphate group. In DNA, the sugar is deoxyribose. In RNA the sugar is ribose. Phosphate is PO 4 2- The bases are one of 5 organic compounds

Deoxyribose Ribose

Nitrogen Bases

DNA Structure DNA forms a double helix structure. That is two complementary strands wrapped around one another is a spiral fashion. The sugar and phosphate form the backbone, while the bases from the rungs. The strands are complimentary because the bases must always be matched up. Adenine and thymine will form a stable hydrogen bond. Guanine and cytosine will also form a stable hydrogen bond. These bases must always be matched up.

DNA Structure

DNA replication When DNA replicates it unwinds and complimentary bases Adenine – Thymine Guanine- Cytosine Are added to a new daughter strand.

Protein synthesis DNA is instructions for building a protein. The DNA is decoded by messenger RNA, mRNA. mRNA then carries the information to the ribosome of a cell. Transfer RNA, tRNA, then adds specific amino acids in order to build the protein.

Lipids Lipids are biochemical compounds defined by being insoluble in water. There are 4 classes of Lipids: Fatty Acids Waxes Phospholipids Steroids

Fatty Acids Fatty acids are carboxylic acid chains. Vegetable oil and animal fats are triglycerides. Triglycerides- esters of glycerol bound to 3 fatty acids The primary function of triglycerides is storage of energy. These fats can be saturated (with hydrogen) They can also be unsaturated, meaning they have double bonds decreasing the amount of hydrogen.

Triglycerides

Phospholipids Phospholipids are similar to triglycerides but only have 2 fatty acids instead of 3. They also have a phosphate group attached to the glycerol. Phospholipids are needed in cell membranes.

Waxes Waxes are long carbon chain esters. They are solids at room temperature. They provide water proof coatings on leaves. They are used in crayons, lip stick, candles, and a variety of other things.

Steroids Steroids are a class of lipids that have a characteristic 4 carbon rings linked together.

Common Steroids Cholesterol- starting material for many steroid molecules. A build up of cholesterol in the arteries has been linked to heart attacks Testosterone- male sex hormone Progesterone/Estrogen- female sex hormones Cortisone- reduces inflammation pain and swelling