1. Organic-Biochemistry
Chapter 1 and Chapter 2
Organic-Biochemistry
Note: Use this ppt. for key concepts from these two chapters.

2. Source of Organic Compounds
There are over six million organic compounds characterized, including the foods we eat, (made of carbohydrates, lipids, proteins, and vitamins), furs and feathers, hides and skins, and the organisms they came from. not to mention plastics, synthetic and natural fibers, dyes and drugs, insecticides and herbicides, ingredients in perfumes and flavoring agents, and petroleum products. The name organic chemistry came from the word organism. Prior to 1828, all organic compounds had been obtained from organisms or their remains.

3. Why are there so many Organic Compounds?
Isomers
Isomerism is another reason why there are so many organic compounds. Isomers are compounds with identical molecular composition but their structures are arranged differently. Depending on how they are arranged, they may have similar or different properties. Because the number of carbons per molecule increases as the compound gets more complex, the number of possible isomers for any given formula becomes very, very large. Formula Number of Isomers
C8H
C10H
C20H ,319
C40H x 1013 (approx.)

4. HONC # of Bonds Mostly: Hydrogen ----1 Oxygen------ 2 Nitrogen-----3
Carbon

6. Structural Formulas Represent covalent bonds with a "line" drawing.
Each "line" represents a pair of shared electrons.
Note: Every carbon has 4 bonds, so "fill-up" with hydrogens if not otherwise noted.
See example below:

7. Recall that a molecular formula (A) describes the numbers of different kinds of atoms in a molecule, and a structural formula (B) represents a two-dimensional model of how the atoms are bonded to each other. Each dash represents a bonding pair of electrons.

8. Structural Formulas continued…
                                

9. Functional Groups

10. Alkanes --Hydrocarbons --examples of 1st 10 alkanes
with naming/structures
--alkyl groups
--IUPAC/common names
--cycloalkanes
--Biological Effects of Alkanes
--Combustion
--Petroleum

12. General Formula: CnH2n+2 Note: 3 ways to write formula:
1. Molecular
2. Structural
3. Condensed
Draw examples on board
Methane
Ethane
Propane
Butane
Pentane
Hexane

13. Introduction
A hydrocarbon is a compound consisting of only hydrogen 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

14. Naming of Alkanes: --find longest continuous chain
--find groups NOT part of longest chain
--assign numbers to groups, giving lowest number possible to groups.
--use prefixes if two or more indentical groups
--if different groups, use alphabetical order
--name other groups (like halogens) by prefixes, such as "chloro" for chrorine.
--See example below

15. Alkyl Groups The name of the alkyl group relates to the alkane
Example: If a CH3 is used, it is a methyl group

16. Alkyl Groups Methyl Group
Methane has one carbon and four hydrogens. The methyl group also has one carbon but only three hydrogens. In place of the fourth hydrogen, there is a bond to something else.methyl
Ethyl Group
Ethane has two carbons and six hydrogens. If any one of those hydrogens is removed and replaced with a bond to something else, you end up with an ethyl group.ethyl

17. Propyl Groups
Propane has three carbons and eight hydrogens. If one of the six end hydrogens is replaced by a bond to something else, you end up with a normal propyl group. If one of the two middle hydrogens is replaced by a bond to something else, you end up with an isopropyl group.

18. Butyl Groups
The next set of alkyl groups contains four carbons. That is why they are called butyl groups. There are four types of butyl groups each with a different combination of carbon chain and bonding point.
The first one is a straight chain with an H missing from the end and is called a normal butyl group (or  n-butyl group). n-butyl or butylThe next one is iso-butyl (usually spelled isobutyl). It has a branched chain at the end opposite where it attaches to something else. iso-butyl or isobutylThere is also a secondary-butyl which is often referred to as sec-butyl. Its structural arrangement is shown here.   sec-butylAlso, tertiary-butyl (also called tert-butyl or t-butyl) has a fourth kind of arrangement as shown.

20. These names are for unbranched alkanes only.
1 methane CH hexadecane CH3(CH2)14CH3
2 ethane CH3CH3 17 heptadecane CH3(CH2)15CH3
3 propane CH3CH2CH3 18 octadecane CH3(CH2)16CH3
4 butane CH3(CH2)2CH3 19 nonadecane CH3(CH2)17CH3
5 pentane CH3(CH2)3CH3 20 eicosane CH3(CH2)18CH3
6 hexane CH3(CH2)4CH3 21 heneicosane CH3(CH2)19CH3
7 heptane CH3(CH2)5CH3 22 docosane CH3(CH2)20CH3
8 octane CH3(CH2)6CH3 23 tricosane CH3(CH2)21CH3
9 nonane CH3(CH2)7CH3 24 tetracosane CH3(CH2)22CH3
10 decane CH3(CH2)8CH3 25 pentacosane CH3(CH2)23CH3
11 undecane CH3(CH2)9CH3 26 hexacosane CH3(CH2)24CH3
12 dodecane CH3(CH2)10CH3 27 heptacosane CH3(CH2)25CH3
13 tridecane CH3(CH2)11CH3 28 octacosane CH3(CH2)26CH3
14 tetradecane CH3(CH2)12CH3 29 nonacosane CH3(CH2)27CH3
15 pentadecane CH3(CH2)13CH3 30 triacontane CH3(CH2)28CH3

21. Cycloalkanes
-carbon atoms are connected in a ring structure instead of a chain.
-name by using prefix "cyclo" before alkane name
-number by using lowest numbers for groups
-see example below

22. (A)The "straight" chain has carbon atoms that are able to rotate freely around their single bonds, sometimes linking up in a closed ring. (B) Ring compounds of the first four cycloalkanes.

23. Practice: Diagram the following Alkanes
a. heptane
b. 3-ethylhexane
c. 4-propylnonane
d. 2,6-dimethyloctane
e. methylcyclobutane

24. Biological Effects of Alkanes
-liquid alkanes dissolve lipids of cell membranes (so swallowing gasoline is dangerous!)
-liquid alkanes will dissolve natural oils in skin (so, gasoline dries out your hands)
-Organic cleaners clean organic substances.
-high-molecular weight alkanes tend to be solid at room temp, so since they are insoluble in water, they will protect skin from drying out--reason for using petroleum jelly ( vaseline)

25. Combustion of Alkanes Fuel + Oxygen yields Carbon Dioxide + Water
(and energy, of course)
Relate this to:
-Aerobic respiration in humans
-burning of fuels such as octane, propane
-emissions tests for cars and the "print-out" showing levels of : Carbon Dioxide, Carbon Monoxide, and Hydrocarbons

26. Gasoline is a mixture of hydrocarbons (C8H18 for example) that contain no atoms of oxygen. Gasohol contains ethyl alcohol, C2H5OH, which does contain oxygen. The addition of alcohol to gasoline, therefore, adds oxygen to the fuel. Since carbon monoxide forms when there is an insufficient supply of oxygen, the addition of alcohol to gasoline helps cut down on carbon monoxide emissions. An atmospheric inversion, with increased air pollution, is likely during the dates shown on the pump, so that is when the ethanol is added.

27. Cars and Gas Laws website for engines

28. Incomplete combustion
Incomplete combustion (where there isn't enough oxygen present) can lead to the formation of carbon or carbon monoxide.
As a simple way of thinking about it, the hydrogen in the hydrocarbon gets the first chance at the oxygen, and the carbon gets whatever is left over!
The presence of glowing carbon particles in a flame turns it yellow, and black carbon is often visible in the smoke. Carbon monoxide is produced as a colorless poisonous gas.
Why carbon monoxide is poisonous
Oxygen is carried around the blood by hemoglobin (US: hemoglobin). Unfortunately carbon monoxide binds to exactly the same site on the hemoglobin that oxygen does.
The difference is that carbon monoxide binds irreversibly - making that particular molecule of hemoglobin useless for carrying oxygen. If you breath in enough carbon monoxide you will die from a sort of internal suffocation.

29. What Pollutants Do Motor Vehicles Emit and What Are the Health Effects?
Motor vehicles generate three major pollutants: hydrocarbons, nitrogen oxides, and carbon monoxide.
Hydrocarbons react with nitrogen oxides in the presence of sunlight and elevated temperatures to form ground-level ozone. It can cause eye irritation, coughing, wheezing, and shortness of breath and can lead to permanent lung damage.
Nitrogen oxides (NOx) also contribute to the formation of ozone and contribute to the formation of acid rain and to water quality problems.
Carbon monoxide is a colorless, odorless, deadly gas. It reduces the flow of oxygen in the bloodstream and can impair mental functions and visual perception. In urban areas, motor vehicles are responsible for as much as 90 percent of carbon monoxide in the air.
Motor vehicles also emit large amounts of carbon dioxide, which has potential to trap the Earth's heat and cause global warning.
Auto emissions EPA website

30. Petroleum and Alkanes Petroleum: -Petroleum is crude oil
-hundreds to thousands of alkanes in crude oil
-must be refined to separate into desired components for specific uses.
Alkanes:
Burning of Alkanes in Cars:
-unbranched cause "knocking"
-branched have higher octane number (see structural formual for iso-octane) and relate this to octane number at gasoline stations.

31. Refinery and tank storage facilities, like this one in Texas, are needed to change the hydrocarbons of crude oil to many different petroleum products.

32. Distillation of Petroleum
Modern distillation involves pumping oil through pipes in hot furnaces and separating light hydrocarbon molecules from heavy ones in downstream distillation towers – the tall, narrow columns that give refineries their distinctive skylines.
The Pascagoula Refinery’s refining process begins when crude oil is distilled in two large Crude Units that have three distillation columns, one that operates at near atmospheric pressure, and two others that operate at less than atmospheric pressure, i.e., a vacuum.
During this process, the lightest materials, like propane and butane, vaporize and rise to the top of the first atmospheric column. Medium weight materials, including gasoline, jet and diesel fuels, condense in the middle. Heavy materials, called gas oils, condense in the lower portion of the atmospheric column. The heaviest tar-like material, called residuum, is referred to as the "bottom of the barrel" because it never really rises.

33. `
Petroleum is a mixture of alkanes, cycloalkanes, and aromatic hydrocarbons.
Petroleum is formed from the slow decomposition of buried marine life, primarily plankton and algae.
As petroleum is formed it is forced through porous rock until it reaches an impervious layer of rock.
Here it forms an accumulation of petroleum and saturated the porous rock creating an oil field.

35. Petroleum products and the ranges of hydrocarbons in each product.