Chemical Compounds for Life

• All living things are mostly composed of 4 elements: H, O, N, C "honk"
• Compounds are broken down into 2 general categories:
o Inorganic Compounds:
 Do not contain carbon
o Organic compounds
 Contain significant amounts of carbon.
 Often found with common "functional groups"
Carbon: The "swiss army knife" of chemistry.

• Carbon is essential to life for several reasons:
1. It can form strong stable (usually nonpolar) covalent bonds
2. It can form up to 4 chemical bonds
3. It can form multiple bonds

• Organic Compounds often form Polymers
o Long chains of smaller molecules (not atoms) called monomers, bind to form huge Macromolecules.
Organic Compounds of life:
• 4 Types: Carbohydrates, Lipids, Proteins & Nucleic acids
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CARBOHYDRATES:
• Includes: Sugars, starches, cellulose & glycogen
• Made of Carbon ( C ), Hydrogen ( H ), and Oxygen (O )
• Following ratio of elements CnH2nOn
o Sugars: Provide & store energy for cells
o Simple sugars include Glucose & Fructose since these are made of only 1 Carbohydrate molecule they are known asMonosaccharides.


• Monosaccharides can be linked together through the process of Dehydration Synthesis
o Water is removed from 2 monocaccharides - resulting in a covalent bond between the 2 molecules
• Sucrose (table sugar) is made of 2 sugars linked together and these are called Disaccharides
o Often referred to as transport saccharides
o Require some digestion to be used by cells

Dehydration Synthesis
• Starches are many monosaccharides linked together in a single chain. These are called Polysaccharides.
o Plants use this for energy storage e.g. Potatoes
o Two types
 Amylose - Long strait unbranched chains
 Pectins - many linked short Amylose chains

Starch
• Cellulose is made of long polysaccharide chains
o Plants use this for structure (e.g. Wood) - not very digestible
o Due to the reverse orientation of the monosaccharide sububnits, digestive enzymes cannot hydrolize the bonds between them

Cellulose

• Glycogen is a moderately branched polysaccharide
o Animals use this for energy storage.

Glycogen

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Lipids:
• Lipids are macromolecules including fats, waxes & oils
o Primary function is energy storage.
 Energy is stored in C-H bonds.
 More efficient in storing energy
o Lipids are made of 2 parts
 Glycerol - an alcohol - Serves as backbone of the molecule
 3 Fatty acids - Long hydrocarbon chains

• Saturated fats have long chains with no double-bonds
• Unsaturated fats have double bonds
• Polyunsaturated fats have many double bonds
• Each time a double bond is encountered, the molecule "Bends" slightly, resulting in a lower density of the lipid. This makes the molecule more likely to remain liquid at room or body temperatures.
• 4 Major types of biologically important Lipids
• Phospholipids - Important for membrane structure
• Steroids - eg. Cholesterol & testosterone. Provide membrane support / serve as hormones
• Terpenes - serve as important components of pigments
• Prostaglandins - appear to act like localized hormones to induce cellular/tissue responses.


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Proteins
• Proteins are made of Amino Acids
• There are 20 different amino acids. Each having a similar general structure - Differ only in their "R" groups


example amino acids
• Amino acids form proteins via deyhdration sythesis forming peptide bonds
• Two amino acids linked together are called dipeptides
• More than 2 linked together are called polypeptides - polypeptides can be thousands of amino acids long

• Protein types include globular proteins which are usually enzymes and Fiberous proteins which usually serve for structure (eg. Hair)
• Proteins Exhibit 4 "levels of structure.

o Primary Structure of a protein is it’s sequence of amino acids.

o The Sequence (primary structure) causes parts of a protein molecule to fold into sheets or bend into helix shapes - this is a protein’s Secondary Structure.

o The protein then can compact and twist on itself to form a mass called it’s Tertiary Structure

o Several Proteins then can combine and form a protein’s Quaternary Structure.

• Various conformations are usually caused by the formation of hydrogen or disulfide bonds
• PH, changes or heat can disrupt these bonds, permanently denaturing the protein.

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Nucleic Acids
• Two types of Nucleic acids
• DNA (Deoxyribonucleic Acid)
• RNA (Ribonucleic acid)
o DNA is Formed of in a "Double Helix" - like a spiral staircase.

DNA Molecule-note "double helix" shape
• DNA is formed by Nucleotides
o These are made from 3 components
 A 5-Carbon Sugar
 A Nitrogenous base
 A Phosphate group

• Nucleotides form a backbone through linkages from the OH group of the 3rd carbon to a phosphate group of the adjoining nucleotide. These are called Phosphodiester bonds

• For DNA There are 4 different Nucleotides categorized as either Purines (double ring) or Pyramidines (single ringed). These are usually represented by a letter. These Are:
o Adenine (A)
o Cytosine (C)
o Guanine (G)
o Thymine (T)


• Each "Rung" of the DNA "staircase" is formed by the linking of 2 Nucleotides through Hydrogen Bonds.
• These Hydrogen bonds form only between specific Nucleotides. This is known as Base Pairing. The rules are as follows:
o Adenine (A) will ONLY bond to Thymine (T)
o Cytosine (C) will ONLY bond to Guanine (G)


• RNA differs from DNA in several important ways.
1. It is much smaller
2. It is single-stranded
3. It does NOT contain Thymine, but rather a new nucleotide called Uracil which will bind to Adenine.


Comparison of DNA & RNA

• ATP is closely related to nucleic acids.
• Composed of Ribose, Adenine & a phosphate group
o Phosphate group has ability to bind/release additional phosphate group allowing it to store or release energy.

Hydrocarbon Derivatives

Organic compounds are divided into two main classes: hydrocarbons and hydrocarbon derivatives
Hydrocarbon-derivative is a compound of carbon molecules and at least one other element that is not hydrogen
-Organic halides are organic compounds in which one or more hydrogen atoms have been replaced by halogen atoms
Public-organic halides including Freon (chlorofluorocarbons) and Teflon (polytetrafluoroethylene)
Naming-halide using the same format as branched-chain hydrocarbons
-The branch is named by shortening the halogen name for fluoro-, chloro-, bromo-, or iodo-
-In the drawing organic halides using IUPAC names, draw the parent chain and add branches in locations specified in the name
for example.
     Cl Cl
      | |
    HCCH
      | |
      HH

  1,2-dikloroetan


Fast-reacting organic halides is described from the idea that there is no strong covalent bonds broken - the rearrangement of electrons does not involve the separation of carbon atoms
Addition of halogen can be added to the resulting alkenes or alkynes alkanes
-By adding a halogen to an alkene, the product can undergo another step Additionally, by adding halogen to the parent chain, bonds should be a single bond to accommodate halogen
for example.

  Br Br Br Br
   | | | |
 HC = CH + Br-Br => HCCH
  | |
                     Br Br


-By adding hydrogen halides to unsaturated compounds will produce isomers
   HHHHHHHHH
   | | | | | | | | |
 HC = CCH + H-Cl => HCCCH OR HCCCH
       | | | | | | |
       HCl Cl H HH H

Substitution-reactions are reactions involving the rupture of the carbon-hydrogen bonds in an alkane or aromatic ring and the replacement of a hydrogen atom by atom or group of atoms
-With light energy allows substitution reaction to move to the level of such looks. C 3 H 8 + BR 2 + light => C 3 H 7 Br + HBR
-Through the substitution reaction, the reaction to the product name, it only shows the number of locations replacement, followed by halogen prefix (eg Bromo-) and then declare the parent chain type. Also shows both created from the reaction product substitution (hydrogen bromide) for example. propane + bromine => 1-bromopropane + hydrogen bromide
-Removal is an organic reaction in which an alkyl halide reacts with the hydroxide ions to produce an alkene by removing a hydrogen ion and a halide of molecules

   Hhhhhh
   | | | | | |
 HCCCH + OH => HC = CCH + + HO Br
   | | | | |
   BRH H HH

-Alcohol has properties that can be explained by the presence of hydroxyl (OH-) functional group attached to the hydrocarbon chain
-Short-chain alcohols are very soluble in water because they form hydrogen bonds with water molecules
-Alcohol is used as a solvent in organic reactions because they are effective for both polar compounds and non-polar
-For the name of the alcohol, the-e is dropped from the final name of alkanes and substituted with-ol for example. Methane => methanol
-Methanol is also called wood alcohol because it never made by heating wood shavings in the absence of air
-Today, methanol is made by combining carbon monoxide and hydrogen at high temperature and pressure using a catalyst
-Methanol, however, is toxic to humans. Consuming small amounts can cause blindness or death
-When naming alcohols with more than two carbon atoms, the position of the hydroxyl group is indicated
Alcohol-containing more than one hydroxyl group is called polyalcohols, such as their name indicates the position of the hydroxyl group. 1,2-ethanediol
-Alcohol undergo elimination reaction to produce alkenes via catalyzed by concentrated sulfuric acid, which removes or eliminates hydrogen atoms and hydroxyl groups
   Hhhh | | | |
 HCCH + acid => HC = CH + HO
   | | |
   H OH H

  acid + ethanol => ethene + water


-Ether is a family of organic compounds that contain oxygen atoms bonded between two groups of hydrocarbons, and has the general formula R-1 OR 2
-To add oxy ether name for the group prefixes for smaller hydrocarbons and join the alkane name of the larger hydrocarbon
for example.
  CH 3-OC 2 H 5

  methoxyethane


-Ether has a low solubility in water, low boiling point, and had no evidence of hydrogen bonding
Ether-chemistry changes when treated with reagents only strong in robust condition
Ether-alcohols formed by a condensation reaction
Condensation-reaction is the joining of two molecules and the elimination of a small molecule, usually water
Carbonyl-functional groups,-CO-, consisting of a carbon atom double-bonded oxygen atoms covalently
-Aldehydes have carbonyl groups at the terminal carbon atom of the chain
-To name an aldehyde, replacing the final-e of the corresponding alkane name with the suffix-al
Small-molecule aldehydes have sharp, irritating odor while larger molecules have the smell of flowers and used to make perfume
-A ketone has a carbonyl group is present everywhere in the carbon chain except at the end of the chain
-The difference in the position of the carbonyl group affects the chemical reactivity, and allows us to distinguish aldehydes from ketones in empirical
-To name a ketone, replacing e-end of the corresponding alkane name with-one
-The simplest ketone is acetone (propanone), CH 3 COCH 3
Family-organic compounds, carboxylic acids containing carboxyl functional group,-COOH, which includes both the carbonyl and hydroxyl groups
-Carboxylic acid found in citrus fruits, and other foods with nature has a sour taste
-Carboxylic acid also has a distinctive odor (like sweat from a person's leg)
-The molecules of carboxylic acids form hydrogen bonds well with the pole and each other and with water molecules
The acid-carboxylic acid, so the litmus test to separate hydrocarbons from other derivative
-To name a carboxylic acid, replacing e-end of the alkane name with-oic, followed by a "sour" said
Methanoic-acid, HCOOH, is the first member of the family of carboxylic acids
Some acid-containing carbonyl groups of two or three such as oxalic acid, and citric acid

     COOH CH 2-COOH
     | |
     COOH HO-C-COOH
|
CH 2-COOH

    
  oxalic acid citric acid


-When carboxylic acids undergo condensation reactions, in which the carboxylic acid combines with other reactants, forming two products - organic compounds and water
-Esterification is a condensation reaction in which a carboxylic acid reacts with an alcohol to produce an ester and water
-Carboxylic acid + alcohol => ester + water
-Ester functional group similar to the acid, except that the hydrogen atoms of the carboxyl group is replaced by a branch of hydrocarbons
-Esther is responsible for the odor of fruits and flowers and is also added to foods for flavor and taste
-To name esters, specify the name of the alkyl group of the alcohol used in the esterification reaction
-Then change the end of the name of the acid "-oic acid" to "-oate"
-Methanol + ethanoic acid => methyl ethanoate + water
-Artificial flavorings are made by mixing synthetic ester to give the same smell of natural ingredients
Amide-A consists of the carboxyl groups attached to the nitrogen atom
-Amides can be formed in a condensation reaction
-Amida occurs in proteins, large molecules found in all living organisms
Peptide-bond joining amino acids together in a protein
-To name amides, alkanes have names with the same number of carbon atoms, by e-ending replaced by the suffix-amide
-Change the ending of the carboxylic acids of the "-oic acid" to-amide to have the results of the same name, for example. ethanamide
-Amin consists of one or more hydrocarbon groups attached to the nitrogen atom
-Through X-ray diffraction revealed that the amine functional group is a nitrogen atom bound by a single covalent bond to one, two, or three carbon atoms
-Amin is a polar substance back very soluble in water because they form strong hydrogen bonds with each other and to water
-Amin had a weird, horrible smell (eg smell of rotten fish)
-Name amines including the names of alkyl groups attached to the nitrogen atom, followed by the suffix-amine for example. methylamine
-Amin with one, two, or three hydrocarbon groups attached to the central nitrogen atom is referred to as primary, secondary, and tertiary
-Primary amine is when a hydrogen atom attached to the nitrogen atom is replaced by a hydrocarbon group
-Secondary amine is when two hydrocarbon groups replace hydrogen atoms and a tertiary amine replacing all the hydrogen atoms with the hydrocarbon
-Amin used in the synthesis of pharmaceuticals
-A group of amines which are found in many plants called alkaloids
-Many alkaloids affect the functioning of the central nervous system of animals
-Substitution - alkane / aromatic halogen + + => organic halide light + hydrogen halide
-Elimination - alkyl halide + OH => alkene + water | + water + halide ion
-Elimination - acid + alcohol => alkene + water

aromatic hydrocarbons

An aromatic hydrocarbon or arena  (sometimes also called aryl hydrocarbon)  is a hydrocarbon with a single bond or a double bond, and between carbon atoms. Configuration 6 carbon atoms in an aromatic compound called benzene rings. Aromatic hydrocarbons can be monocyclic or polycyclic.
Some aromatic compounds that are not called heteroarena benzene derivatives, these compounds mengikutiAturan Hückel. In these compounds, at least one carbon atom is replaced by another atom, such as oxygen, nitrogen, or sulfur. One contohn compound is furan, a heterocyclic ring compound having 5 members, one oxygen atom. Another example is pyridine, a heterocyclic ring compound with 6 members, one nitrogen atom.
In aromatic substitution, 1 substituents on the ring arena (usually hydrogen) will be replaced with other substituents. 2 main types are electrophilic aromatic substitution (active electrophile reagent) and nucleophilic aromatic substitution (reagennya nucleophile). Padasubstitusi radical-nucleophilic aromatic, active form of radical reagents. One example is the nitration of salicylic acid:

Benzene (C6H6) is the parent compound of a large class of these organic substances.

Benzene molecules form a flat hexagon with carbon atoms located on the sixth corner. All the same carbon-carbon bond length and strength, as well as all the carbon-hydrogen bonds, and all the angles CCC and HCC is 1200. Thus, each carbon atom sp2 hybridise, every atom that form three sigma bonds with two carbon atoms next to them and the hydrogen atom. This arrangement leaves one that did not hybridise 2pz orbital on each carbon atom, perpendicular to the plane of the molecule of benzene or benzene ring. In the ethylene molecule, overlapping two 2pz orbitals produces a bonding molecular orbital and one antiikatan molecular orbitals, which are localized in both atom C. However, 2pz orbital interactions in benzene leads to the formation of delocalized molecular orbitals, which are not confined between two adjacent atoms bonded to each other, but also extends to three or more atoms.
Benzene molecule can undergo substitution reactions. If benzene with one H atom is replaced by one atom to another atom group called monosubstituen. For example: etilenbenzena, chlorobenzene, aminobenzena, nitrobenzene, hidroksibenzena, and many more with different groups.

chlorobenzene ethylbenzene aminobenzena hidroksibenzena
(Aniline) (phenol)
If benzene with two H atoms is replaced by another atom or group called disubstituen and produce three kinds of isomers based on the location of the two groups. If the two adjacent groups called ortho, if the two groups are separated one C atom is called meta, and if the two groups separated by two C atoms is called the. Group replaces the H atom in benzene can be the same or different which enables the production of benzene derivative compounds as much as a part of the carbon compounds.

dibromobenzena ortho-meta-para-dibromobenzena dibromobenzena
A large number of compounds can be made from substances that are combined with the benzene ring. The most famous of these compounds are naphthalene, used in mothballs. These compounds and many other similar compounds found in coal tar. Several compounds with multiple rings is a strong carcinogen-compound can cause cancer in humans and animals

Why carbon atoms tend to bind duplex

why it tends to bind carbon copies?

this can be explained by the theory of hybridization, in which the theory is able to explain the fatal pull of the C - H, for example, the methane (CH4), which is a simple hydrocarbon compounds, in which the four electrons from four H atoms are not just given to four valence electrons of carbon but there is a process of hybridization, and this is what causes it to become carbon double bond, either in a single or triplicate, and the dual iktan who do not have the orbital hybridization, and this theory can only predict but not could explain why the reaction can occur

the carbon atom bonded neighbors can occur 3 possibility :

1. carbon atoms form a single bond

     this happens in the orbital S and called a sigma bond hybrid orbitals SP3 and tetrahedron-shaped   molecule with an angle of 109.5 degrees. This compound is called saturated hydrocarbons

2. carbon atoms form a double bond

    occurred in the orbital P and is called a pi bond. angle changes due to two orbital P orbitals SP2 parallel to form an angle of 120 degrees

3. carbon atoms form a triple bond

     there are 2 orbitals of P in parallel so as to change the orbital position of the SP to form an angle of 180 degrees planar

petroleum

Petroleum and natural gas thought to have come from the ocean microorganisms, plants and animals that died about 150 million years ago. The assumption is based on the similarity of the elements contained in these materials with elements found in living things. The remains of organisms that settle on the sea floor, then covered with mud which gradually hardens as a layer above the pressure that turned into rock. Meanwhile, anaerobic bacteria decompose the remains of organisms that an oil and gas trapped between the layers of the earth's crust. The process of the formation of oil and gas it takes a very long time. Even during our age is not enough to make oil and gas. So we have to make savings and trying to find alternative energy sources.


The composition of petroleum

Oil drilling is still a result of crude oil (crude oil) is thick and black. Crude oil consists of a mixture of hydrocarbons that
Alkanes
Alkane compounds most commonly found is the n-octane and isooctane (2,2,4-trimethyl pentane)
AromatisDiantaranya hydrocarbons is the ethyl benzene
Among other cycloalkanes ethyl cyclopentane and cyclohexane
Sulfur (0.01 to 0.7%)
Nitrogen (0.01 to 0.9%)
Oxygen (from 0.06 to 0.4%)
Carbon dioxide [CO2]
Hydrogen sulfide [H2S]


Petroleum processing

Petroleum is usually beradai 3-4 km below the surface. To take the oil we have to make boreholes that had been adjusted depth. Crude oil gained tangker accommodated in the ship or supplied to the refinery by using a pipe. Crude oil that had been obtained can not be used as a fuel or other purposes. Crude oil must be processed first. Crude oil contains about 500 types of hydrocarbons by the number of atoms C-1 to C-50. Petroleum processing through distillation storey, where crude oil is separated into groups with similar boiling points. This is done because the boiling point hydrocarbons increases with the carbon atoms (C) in the molecule.
At first, Crude oil is heated at a temperature of about 400C. After heated later in the stream to the tower fractionation / distillation
Distillation tower
Dimenara is a process of distillation. Namely the separation solution using heat as a separator. The main requirement is that the distillation process is the difference in composition between the liquid phase and vapor phase. Thus, if the composition of the liquid phase and vapor alike face the distillation process is not possible. The process of distillation in petroleum refineries is the primary processing of physics as the beginning of the process of producing the fuel (fuel oil).




Refining scheme


Crude oil is the result of drilling in the stream to the ship tangker and then distributed to the refinery. This is where the process of distillation which has been in jalaskan above. First, Crude heated to a temperature of about 400 degrees C. Components of a higher boiling point will remain a liquid and will flow down to the bottom, while the boiling point will evaporate more randah rise up through the containment lid-lid-called bubble. Getting up the temperature in the fractionation tower was getting low. Thus, each time the component with a higher boiling point rise, it will condense and separate, while the components with a lower boiling point will continue to rise into the upper part again. So it went on, so the above components in the form of gas. Components in the form of gas is called petroleum gas. Then the liquefied petroleum gas and dikelan as LPG (Liquefied Petroleum Gas).

The results of refined petroleum


Of the scheme on the previous page we can see the results from the distillation of crude oil. Diatnaranya namely:

LPG
Liquefied Petroleum Gas (LPG) with Pertamina ELPIJI brand, is the result of gas production from refineries (refinery fuel) and gas refinery, which is the main component of propane (C3H8) and butane (C4H10) approximately 99% and the rest is gas pentane ( C5H12) were thawed

Aviation fuel
One aviation fuel aviation fuel which is used as fuel persawat fly.

Gasoline
Gasoline is a fuel transport still plays an important role to date. Gasoline containing more than 500 types of hydrocarbons having chain C5-C10. Levels vary depending on the composition of the crude oil and desired quality.

Kerosene (kerosene)
Hydrocarbon fuels obtained as petroleum distillates with a higher boiling point than gasoline; kerosene; patra oil.

Diesel fuel
Diesel, in Indonesia, better known as solar, is an end product which is used as a fuel in a diesel engine invented by Rudolf Diesel, and perfected by Charles F. Kettering.

Lubricants
Lubricants are chemical substances, which are generally fluid, which was given between two moving objects to reduce friction. Lubricant serves as a protective layer that separates the two surfaces touch

Candle
Candle is a light source consisting of a wick covered by solid fuel. The fuel used is paraffin

Fuel oil
Fuel oil is distilled from petroleum refining but has not yet formed the final residue of the refining process itself. Usually the color of oil is black chrome. Besides oil more dense than diesel oil

Asphalt
Asphalt is the material that is attached to the hydro carbon (adhesive), brownish-black, water resistant, and visoelastis. Asphalt is often called bitumen binder in asphalt mixture



The negative impact of the use of petroleum

Air Pollution
Decline in air quality due to the waste from the use of petroleum

Climate change
The use of petroleum will produce the waste in the form of CO2 ¬. Gas can cause the greenhouse effect in the earth so that there are now global warming is happening. Global warming is exactly what caused climate change in various world balahan

Water pollution
Exploitation of oil earth using tangker ship, did not rule out the existence of a leak in the ship tangker. Because the ship was leaking tangker, the crude oil is inside will come out and fall keair causing water pollution.