Organic Compounds, Polymers, and Biochemicals

Organic chemistry is the study of the preparation, properties, and reactions of those compounds of carbon not classified as inorganic. The uniqueness of element carbon are carbon atoms have ability to form strong covalent bonds to each other while at the same time bonding strongly to atoms of other nonmetals. The carbon atoms are also can form different structure from identical molecular formulas which called isomerism.

Compound structure of the carbon atoms are divided into three structures, there are continuous sequence of carbon atoms which called straight chain. The branched chains is the structur of carbon atoms which have branches. Carbon ring or cyclic is the structure of carbon atoms which have closed structure. Functional groups are small structural units within molecules at which most of the compound’s chemical reactions occur. the functional groups are shown attached to the symbol R. symbol R in a structure is to represent purely alkane-like hydrocarbongroups, which are unreactive toward substances that are able to react with the functional group.

Hydrocarbons are compounds whose molecules consist of only C and H atoms. Hydrocarbons can be divided into four types: alkanes, alkenes, alkynes, and aromatic hydrocarbons. The alkanes, mentioned earlier, contain carbon atoms bonded to other atoms by only single bonds. Open-chain members of the alkane family have the general formula C_nH_2n+2. The alkenes contain one or more carbon–carbon double bonds and general formula of alkene family is C_nH_2n. The alkynes contain one or more triple bonds and general formula of alkyne family is C_nH_2n-2. Alkenes and alkynes are said to be unsaturated compounds because under appropriate conditions their molecules can take up additional H atoms to give alkane molecules. The alkanes are saturated compounds, compounds with only single bonds, and do not take on additional H atoms. The aromatic hydrocarbons, typified by benzene, are also unsaturated because the carbon atoms of their rings, when represented by simple Lewis structures, also have double bonds.

Alkanes are relatively unreactive at room temperature and it can’t react with concentrated acids or concentrated aqueous bases. Alkanes burn in air to give water and oxides of carbon (CO₂ and CO). Hot nitric acid, chlorine, and bromine also react with alkanes. When heated at high temperatures, alkanes can break up into smaller molecules. IUPAC rules for naming the alkanes, the name ending for all alkanes (and cycloalkanes) is –ane. The parent chain is the longest continuous chain of carbons in the structure. A prefix is attached to the name ending, -ane, to specify the number of carbon atoms in the parent chain. Any branch that consists only of carbon and hydrogen and has only single bonds is called an alkyl group, alkyl group is an alkane minus one of its hydrogen atoms.

Alkenes and Alkynes are virtually nonpolar, therefore insoluble in water and they are flammable. IUPAC nomenclature of alkenes and alkynes, the parent chain must include the double bond even if this means that the parent chain is shorter than another. The parent alkene chain must be numbered from whichever end gives the first carbon of the double bond the lower of two possible numbers. The parent chain name of alkene or alkyne is –ene or –yne. The numbers for the locations of branches are not considered in numbering the chain. Otherwise, alkyl groups are named and located as before. Some alkenes have two double bonds and are called dienes. Some have three double bonds and are called trienes, and so forth. Each double bond has to be located by a number. Geometric Isomerism is made by lack of free rotation at a carbon-carbon double bond. Geometric isomerism is divided into cis and trans geometric isomerism, Cis means “on the same side;” trans means “on opposite sides.”

Aromatic Hydrocarbons, the most common aromatic compounds contain the benzene ring, a ring of six carbon atoms, each bonded to one H or one other atom or group. Aromatic hydrocarbons like benzene, do not give the addition reactions shown by alkenes. Instead, they undergo substitution reactions that leave the energy lowering, π electron network intact. In the presence of suitable catalysts, benzene undergoes these Reactions with chlorine, bromine, nitric acid, and sulfuric acid.

Alcohols have general structure, that is ROH, with R is symbol to represent any alkyl group. And also Ethers, the general structure of it is ROR^I, with R and R^I is don’t have to be same. In naming of alcohols, the parent chain is the longest that includes the carbon holding the OH group. The name ending for alcohol is –ol. The reaction of alcohols and ethers, ethers are almost as chemically inert, they can burn, and they are split apart when boiled in concentrated acids. The oxidation of an alcohol with RCH₂OH type can form aldehyde, which is further oxidized to a carboxylic acid. The oxidation of an alcohol of the R₂CHOH type can produces a ketone. But alcohol with R₃COH type cannot be oxidized in a similar manner. An alcohol molecule can undergo the loss of a water molecule, leaving behind a carbon–carbon double bond. This reaction, called dehydration. An alcohol can also has substitution reactions, the OH group can be replaces by a halogen atom using a concentrated strong binary acid.

Aldehydes and Ketones are formed by oxidation of alcohols. The general structure of Aldehydes is RCO=H, and the general structure of Ketone is RCOR^I. The naming of Aldehydes and Ketones, The IUPAC name ending of aldehydes is –al and the parent chain is the longest chain that includes the aldehyde group. The name ending of Ketone in IUPAC names is –one. The reactions of Aldehydes and Ketones, hydrogenation or reduction is abiut addition of hydrogen across the double bond of an alkene and takes place under roughly the same conditions.

Carboxylic Acids and Esters, Carcoxylic acid (RCOOH) and Ester (RCOOR^I). The naming of Carboxylic acids and Esters, the name ending of carboxylic acid is –oic acid and the name ending of ester is –ate. The reactions of carboxylic acids and esters, The carboxyl group is weakly acidic and neutralize Brønsted bases such as the hydroxide, bicarbonate, and carbonate ions.Ester can formed by heating a solution of the parent carboxylic acid and the alcohol in the presence of an acid catalyst. Esters are also split apart by the action of aqueous base, only now the carboxylic acid emerges not as the free acid but as its anion. The reaction is called ester saponification.

Organic Derivatives of Ammonia, Amines are able to dissolve in water establish an equilibrium in which a low concentration of hydroxide ion exists. Carboxylic acids can also be converted to amides, a functional group found in proteins. In amides, the OH of the carboxyl group is replaced by nitrogen, which may also be bonded to any combination of H atoms or hydrocarbon groups.

A polymer is macromolecular substance whose molecules all have a small characteristicstructural feature that repeats itself over and over. The repeating unit of a polymer is contributed by a chemical raw material called a monomer and reaction that makes a polymer out of a monomer is called polymerization. There are two ways of polymerization, addition and condensation.  Addition is polymerization by severing the double bond, while condensation is polymerization by eliminating two monomer to joined. Nylons and polyesters are copolymers because they are formed from two different monomers. The polymerization of ethylene can lead to branching, which produces an amorphous polymer called low-density polyethylene (LDPE). High-density polyethylene (HDPE) and ultrahighmolecular- weight polyethylene (UHMWPE) are not branched and are more crystalline, which makes them stronger. Nylon’s properties are affected by hydrogen bonding between polymer strands.

Carbohydrates, the simpler unit of it is called monosaccharides and the example of it is glucose. Carbohydrates whose molecules are split into two monosaccharide molecules by reacting with water are called disaccharides, sucrose is the example. A polysaccharide is a type of large polymeric sugar molecule, amylase is the example. Cellulose is a polymer of glucose, much like amylose, but with the oxygen bridges oriented with different geometries.

Lipids are natural products that are water insoluble, but tend to dissolve in nonpolar solvents such as diethyl ether or benzene. The lipid family includes the edible fats and oils in our diets—substances such as olive oil, corn oil, butterfat, and lard. These are triacylglycerols, which are esters between glycerol, an alcohol with three OH groups, and any three of several long-chain carboxylic acids. often unsaturated fatty acids. In the digestion of the triacylglycerols, the hydrolysis of the ester groups occurs, and anions of fatty acids form (together with glycerol).Molecules of glycerophospholipids have large segments that are hydrophobic and others that are hydrophilic. Glycerophospholipid molecules are the major components of cell membranes, where they are arranged in a lipid bilayer.

Proteins Proteins are a large family of substances that make up about half of the human body’s dry weight. They are found in all cells and serve as enzymes, hormones, and neurotransmitters. The dominant structural units of proteins are macromolecules called polypeptides, which are made from a set of monomers called a-amino acids. Many proteins consist of a single polypeptide. Most proteins, however, involve assemblies of two or more polypeptides. Hemoglobin is made of four polypeptides—two similar pairs— and four molecules of heme, the organic compound that causes the red color of blood. The final shape of a protein, called its native form, is as critical to its ability to function as anything else about its molecular architecture.

Enzymes are catalysts in living cells, and virtually all are proteins. Some enzymes require a metal ion, such as Mn²⁺, Co²⁺, Cu²⁺, or Zn²⁺, and also require molecules of the B vitamins to be complete enzymes. Some of our most dangerous poisons work by deactivating enzymes, such as Hg²⁺ and Pb²⁺.

Nucleic Acids are polypeptides of an organism are made under the chemical direction of a family of compounds. The nucleic acids occur as two broad types: RNA, or ribonucleic acids, and DNA, or deoxyribonucleic acids. Nucleic acids are polymers whose backbones are made of a repeating sequence of pentose sugar units. On each sugar unit is a base, a heterocyclic amine such as adenine (A), thymine (T), guanine (G), cytosine (C), or uracil (U). In DNA, the sugar is deoxyribose, and the bases are A, T, G, and C. In RNA, the sugar is ribose and the bases are A, U, G, and C. DNA exists in cell nuclei as double helices. The two strands are associated side by side, with hydrogen bonds occurring between particular pairs of bases. In DNA, A is always paired to T; C is always paired to G. The base U replaces T in RNA, and A can also pair with U. The bases, A, U, G, and C, are the four letters of the genetic alphabet, and the specific combination that codes for one amino acid in polypeptide synthesis are three bases, side by side, on a strand. The replication of DNA is the synthesis by the cell of exact copies of the original two strands of a DNA double helix.

Reference
Brady, James E dkk. (2009). Chemistry: The Molecular Nature of Matter. United states of Amerika: John Wiley and Sons, Inc.