Organic Chemistry Introduction for Nurses BSN Post RN

Organic Chemistry and Introduction For Nurses

Introduction to organic and hydrocarbons for BSN and Posr-RN students.

Organic compounds

    In early 19th century, Swedish chemist Jacob Berzellius put forward the “Vital Force Theory”.According to this theory, organic compounds could not be prepared in laboratories because they were supposed to be synthesized under the influence of a mysterious force called Vital Force, inherent only in living things.

    The Vital Force theory suffered death blow in 1828 when Wohler synthesized the firstorganic compound urea from inorganic substance by heating ammonium cyanate (NH₄CNO):

Organic chemistry

    The branch of chemistry which deals with the study of hydrocarbons and their derivatives is known as organic chemistry.

There are four types of formulae of organic compounds:

• Molecular formula

• Structural formula

• Condensed formula

• Dot and cross formula

Molecular Formula

    The formula which represents the actual number of atoms in one molecule of the organic compound is called the molecular formula, e.g., molecular formula of butane is C₄H₁₀. It shows:

a. Butane is made up of carbon and hydrogen atoms.

b. Each molecule of butane consists of 4 carbon atoms and 10 hydrogen atoms.

Structural formula

    Structural formula of a compound represents the exact arrangement of the different atomsof various elements present in a molecule of a substance. In a structural formula, singlebond is represented by a single line (-), a double bond by two lines (=) and a triple bond bythree lines () between the bonded atoms. Organic compounds may have same molecularformulae but different structural formulae, e.g., structural formulae of butane C₄H₁₀ are:

Condensed Formula

    The formula that indicates the group of atoms joined together to each carbon atom in a straight chain or a branched chain is called the condensed formula.

Electronic or Dot and Cross Formula

    The formula which shows the sharing of electrons between various atoms in one molecule of the organic compound is called dot and cross formula or electronic formula.

Classification of Organic Compounds

    All known organic compounds have been broadly divided into two categories depending upon their carbon skeleton. These are:

(i) Open chain or a cyclic compounds.

(ii) Closed chain or cyclic compounds.

(i) Open chain or a cyclic compounds

    Open chain compounds are those in which the end carbon atoms are not joined with each other, in this way they form a long chain of carbon atoms. These chains may be either straight or branched.For example,

(a) Straight chain compounds are those in which carbon atoms link with each other through a single, double or triple bond forming a straight chain such as;

(b) Branched chain compounds are those in which there is a branch along a straight chain, such as:

Open chain compounds are also called aliphatic compounds.

Closed chain or Cyclic compounds

    Closed chain or cyclic compounds are those in which the carbon atoms at the end of the chain are not free. They are linked to form a ring. They are further divided into two classes:

(a) Homocyclic or carbocyclic compounds.

(b) Heterocyclic compounds.

(a)Homocyclic or Carbocyclic compounds.

    Homocyclic or carbocyclic compounds contain rings which are made up of only one kindof atoms, i.e., carbon atoms. These are further divided into two classes:

• Aromatic compounds

• Alicyclic compounds

Aromatic compounds:

    These organic compounds contain at least one benzene ring in their molecule. A benzenering is made up of six carbon atoms with three alternating double bonds. They are calledaromatic because of aroma or smell they have. For example:

They are also called benzenoid compounds.

Alicyclic or non-benzenoid compounds:

    Carbocyclic compounds which do not have benzene ring in their molecules are calledalicyclic or non-benzenoid compounds. For example,

    (b) Heterocyclic compounds

Cyclic compounds that contain one or more atoms other than that of carbon atoms in theirrings are called heterocyclic compounds.

Properties of Organic Compound

    Organic compounds have the following general characteristics:

(i) Origin: Naturally occurring organic compounds are obtained from plants and animals.On the other hand, inorganic compounds are obtained from minerals and rocks.

(ii) Composition: Carbon is an essential constituent of all organic compounds. They aremade up of few elements such as carbon, hydrogen, nitrogen, oxygen, halogen, Sulphur,etc. On the other hand, inorganic compounds are made up of almost all the elements ofthe Periodic Table known so far.

(iii) Covalent linkage: Organic compounds contain covalent bonds, that may be polar ornon-polar, while the inorganic compounds mostly contain ionic bonds.

(iv) Solubility:Organic compounds having non-polar linkages are generally soluble in organic solvents likealcohol, ether, benzene, carbon disulphide etc. On the other hand, the inorganic compoundswith ionic bonds are soluble in polar solvents like water.

(v) Electrical conductivity:Due to the presence of covalent bonds, organic compounds are poor conductors of electricity,whereas inorganic compounds being ionic in nature, are good conductors of electricity in molten state or in aqueous solution.

(vi) Melting and boiling points: Generally, organic compounds have low melting and boiling points and are volatile in nature. Inorganic compounds, on the other hand, have comparatively high melting and boiling points.

(vii) Stability: Since organic compounds have low melting and boiling points, they are less stable than inorganic compounds.

(viii) Combustibility: Organic compounds with high percentage of carbon are generally combustible. On the other hand, inorganic compounds are mostly non-combustible.

(ix) Isomerism: A main characteristic of organic compounds which differentiate them from inorganic substances is their tendency to exhibit the phenomenon of isomerism. Isomerism is rare in inorganic substance.

(x) Rate of reaction: Due to the presence of covalent linkages, the reactions of organic compounds are molecular in nature. They are often slow and require specific conditions such as temperature, pressure or catalyst.

International Union Nomenclature of Alpha

    IUPAC nomenclature is based on naming a molecule's longest chain of carbons connected by single bonds, whether in a continuous chain or in a ring. All deviations, either multiple bonds or atoms other than carbon and hydrogen, are indicated by prefixes or suffixes according to a specific set of priorities.

    α (Alpha) – the name given to the configuration of a cyclic sugar where the oxygen on the anomeric carbon is on the opposite face of the ring relative to the substituent on the other carbon flanking the ring oxygen. Contrasted with beta (β) which is where the two substituents are on the same faces of the ring.

Compounds (IUPAC)

    In order to name organic compounds, you must first memorize a few basic names. These names are listed within the discussion of naming alkanes. In general, the base part of the name reflects the number of carbons in what you have assigned to be the parent chain. The suffix of the name reflects the type(s) of functional group(s) present on (or within) the parent chain. Other groups which are attached to the parent chain are called substituents.

Alkanes - saturated hydrocarbons

Alkenes and Alkynes - unsaturated hydrocarbons

·        Alcohols

·        Ethers

·        Aldehydes

·        Ketones

·        Carboxylic Acids

·        Amines

Functional Groups

    An atom or group of atoms or presence of double or triple bond which determines the characteristic properties of an organic compound is known as the functional group.

    For example, -OH group is the functional group of alcohols, which givescharacteristics properties of alcohols. The characteristic properties of carboxylic acids are dueto the presence of -COOH group in them. Therefore, functional group of carboxylic acids is-COOH group.

    In an organic compound, firstly, the functional group is identified which gives us the appropriate suffix. Then the longest carbon chain having the functional group is chosen in such a manner that the functional group gets the lowest number in the chain. The priority list of the functional group can be given as:

-COOH > -SO₃H > -COOR (R= alkyl group) > -COCl > -CONH₂ > -CN > -HC=O >>C=O > -OH > -NH₂ >  >C=C<> -CC-

    Functional groups like -R, C₆H₅-, halogens (F, Cl, Br, I), -NO₂, alkoxy (-OR) etc., are always used as prefix substituents.

    If more than one same functional group is present in the compound, then they are indicated as di, tri, … etc. before the suffix and full name of the parent alkane is written.

1)Name the compound given below.

·            In this compound, the functional group present is –OH.

·            The longest chain which contains the functional group has 8 carbon atoms. Hence, the saturated hydrocarbon is octane.

·            The alcohol functional group is present on the 3rd position, and a methyl group is on the 6^th position.

·            Hence, the IUPAC name will be 6- Methyloctan-3-ol.

2)Name the functional group given below:

    This compound has the functional group as ketone (>C=O). Hence, the suffix will be one. And there are two ketone groups. So, we will use di- before suffix as Dione. Continuing in the same manner as above we get the name Hexane-2, 4-dione.

Names, Molecular, Condensed and Structural Formulae of the first ten Hydrocarbon

Sources Of Organic Compound

    Organic compounds are prepared naturally by animals and plants. Animals synthesize two main groups of organic compounds: proteins and fats. Proteins are meat, mutton, chicken and eggs, etc. Fats are present in milk, butter, etc. Plants synthesize; carbohydrates, proteins, fats, vitamins, etc.

 Moreover, dead plants buried under Earth’s crust are converted through biochemical processes to coal, petroleum and gas. These materials are the main sources of organic compounds. We can get thousands of organic compounds by the destructive distillation of coal and fractional distillation of petroleum. Details of each source are given in figure below:

Formation of Alkyl Radicals

    Alkyl radicals are derivatives of alkanes. They are formed by the removal of one of the hydrogen atoms of an alkane and are represented by a letter ‘R’. Their name is written by replacing “ane” of alkane with ‘yl’  represents first ten alkanes and their alkyl radicals. Their general formula is Cn H_2n+1

    It is better to explain the type of radicals of propane and butane. Propane has a straight chain structure. When terminal H is removed, it is called n-propyl. When hydrogen from central carbon is removed, it is called isopropyl, as explained below:

Similarly, different structures of butyl radicals are explained:

Hydrocarbon

    A hydrocarbon is an organic compound consisting of hydrogen and carbon found in crude oil, natural gas, and coal. Hydrocarbons are highly combustible and the main energy source of the world. Its uses consist of gasoline, jet fuel, propane, kerosene, and diesel, to name just a few.

Types of Hydrocarbons

    There are two types of hydrocarbons: aliphatic and aromatic. The three types of aliphatic hydrocarbons are alkanes, alkenes, and alkynes. Aromatic hydrocarbons include benzene. Overall, examples of hydrocarbons are methane, ethane, propane, and butane.

Alkanes

In organic chemistry, an alkane, or paraffin, is an acyclic saturated hydrocarbon. In other words, an alkane consists of hydrogen and carbon atoms arranged in a tree structure in which all the carbon–carbon bonds are single. Alkanes have the general chemical formula CₙH₂ₙ₊₂.

Alkane as saturated hydrocarbons

    Alkanes are a series of compounds that contain carbon and hydrogen atoms with single covalent bonds. These are known as saturated hydrocarbons. This group of compounds consists of carbon and hydrogen atoms with single covalent bonds. Also comprises a homologous series having a molecular formula of CnH2n+2.

    Alkanes are the simplest family of hydrocarbons. They contain only carbon and hydrogen. Each carbon atom forms four bonds and each hydrogen atom forms one bond. Chemists use line-angle formulas because they are easier and faster to draw than condensed structural formulas. Structural formulas for alkanes can be written in yet another condensed form.

    The simple alkane methane contains one carbon atom and CH₄ as its molecular formula. As this compound have just single covalent bonds only, therefore, its structural formula is

Alkenes and alkynes

    Alkenes have at least one carbon-carbon double bond. Alkynes have one or more carbon-carbon triple bonds. Alkenes and alkynes are called as unsaturated hydrocarbons.

    Alkenes have at least one carbon-carbon double bond. Alkynes have one or more carbon-carbon triple bonds. Alkenes and alkynes are called as unsaturated hydrocarbons.Examples: Methane (CH₄), ethane (C₂H₆) is an example of alkanes. Propane (C₃H₈), and ethene are examples of alkene. Ethyne and propyne are examples of alkyne.

Isomerism

    In chemistry, isomers are molecules or polyatomic ions with identical molecular formula – that is, same number of atoms of each element – but distinct arrangements of atoms in space. Isomerism is existence or possibility of isomers. Isomers do not necessarily share similar chemical or physical properties.

e.g., 1-pentene and 2-pentene are isomers

        CH₃​CH₂​CH_2​CH=CH₂​(1-Pentene) & CH3​CH2​CH=CHCH3​(2-Pentene)

Types of isomerism:

1.Structural isomerism

2. Chain isomerism

1.Structural isomerism

1. Compounds having same molecular formula but different structures are classified as structural isomers and phenomenon is called as structural isomerism.

Example: 1-PenteneCH₃​CH₂​CH_2s​CH=CH₂​

                2-Pentene CH_3​CH₂​CH=CHCH₃

_​

2. Chain isomerism

1.When two or more compounds have similar molecular formula but different carbon skeletons, these are referred as chain isomers and the phenomenon is chain isomerism.

Example: Pentane, Isopentane, Neopentane.

Functional groups containing carbon, hydrogen and oxygen

Functional Group Containing Carbon, Hydrogen and Halogens:

The organic compounds having functional group containing carbon, hydrogen and halogens are called alkyl halides. Their functional group is R-X. ‘X’ may be F, CI, Br or I

Macromolecule of human body

    Proteins:In a cell, the most abundant macromolecules are proteins. Proteins are long chains of amino acids essential for many biological functions, including structural support, enzymatic activity, and signaling. They are involved in almost every aspect of cellular function and are present in large quantities within cells.

    Carbohydrates: Most people are familiar with carbohydrates, one type of macromolecule, especially when it comes to what we eat. To lose weight, some individuals adhere to “low-carb” diets. Athletes, in contrast, often “carb-load” before important competitions to ensure that they have enough energy to compete at a high level. 

    Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources of carbohydrates. Carbohydrates provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. Carbohydrates also have other important functions in humans, animals, and plants.

    Lipids: Lipids include a diverse group of compounds that are largely nonpolar in nature. This is because they are hydrocarbons that include mostly nonpolar carbon–carbon or carbon–hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), or insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats.

    Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic birds and mammals dry when forming a protective layer over fur or feathers because of their water-repellant hydrophobic nature. Lipids are also the building blocks of many hormones and are an important constituent of all cellular membranes. Lipids include fats, oils, waxes, phospholipids, and steroids.

Nucleic acids:Nucleic acids are the most important macromolecules for the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell.

DNA and RNA

    The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is found in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope.

    In the other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus but instead use an intermediary to communicate with the rest of the cell. This intermediary is the messenger RNA (mRNA). Other types of RNA—like rRNA, tRNA, and microRNA—are involved in protein synthesis and its regulation.

    DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group. Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.

DNA Double-Helix Structure

    DNA has a double-helix structure. The sugar and phosphate lie on the outside of the helix, forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a staircase, in pairs; the pairs are bound to each other by hydrogen bonds. 

    Every base pair in the double helix is separated from the next base pair by 0.34 nm. The two strands of the helix run in opposite directions, meaning that the 5′ carbon end of one strand will face the 3′ carbon end of its matching strand. (This is referred to as antiparallel orientation and is important to DNA replication and in many nucleic acid interactions.)