The basics of organic chemistry
When you explore biology, you’ll find that many processes are constantly occurring in living organisms. The study of organic chemistry — which focuses on carbon molecules — is central to all living organisms.
The ability to convert ingested fuel to usable energy is what differentiates a living organism from a dead one. The ingested fuel contains a variety of large molecules (macromolecules) that get broken down. When the macromolecules have been broken down into their smallest parts, they can enter the cells, which contain more macromolecules, which are involved in more processes.
What is organic chemistry?
In organic chemistry, the focus is on the element carbon. Carbon is central to all living organisms; however, thousands of nonliving things (such as drugs, plastics, and dyes) are made from carbon compounds.
Diamonds are carbon atoms in a crystal structure. Diamonds are so hard because the atoms of carbon are so closely bonded together in the crystal form. That same ability to pack closely together makes carbon an excellent structural element in its other forms as well.
One atom of carbon can combine with up to four other atoms. Therefore, organic compounds usually are large and can have several atoms and molecules bonded together. Organic molecules can be large, and they comprise the structural components of living organisms: carbohydrates, proteins, nucleic acids, and lipids.
Carbon is key
In their outer shells, carbon atoms have four electrons that can bond with other atoms. When carbon is bonded to hydrogen (which is common in organic molecules), the carbon atom shares an electron with hydrogen, and hydrogen likewise shares an electron with carbon. Carbon-hydrogen molecules are referred to as hydrocarbons. Nitrogen, sulfur, and oxygen also are often joined to carbon in living organisms.
Long carbon chains = low reactivity
Large molecules form when carbon atoms are joined together in a straight line or in rings. The longer the carbon chain, the less chemically reactive the compound is. However, in biology, other measures of reactivity are used. One example is enzymatic activity, which refers to how much more quickly a certain molecule can allow a reaction to occur.
One key to knowing that a compound is less reactive is that its melting and boiling points are high. Generally, the lower a compound’s melting and boiling points, the more reactive it is.
For example, the hydrocarbon methane, which is the primary component of natural gas, has just one carbon and four hydrogen atoms. Because it is the shortest carbon compound, it has the lowest boiling point (-162°C) and is a gas at room temperature. It is highly reactive.
On the other hand, a compound made of an extremely long carbon chain has a boiling point of 174°C (compared to water, which has a boiling point of 100°C). Because it takes so much more for it to boil, it is much less reactive and is not gaseous at room temperature.
Forming functional groups based on properties
In organic chemistry, molecules that have similar properties (whether they are chemical or physical properties) are grouped together. The reason they have similar properties is because they have similar groups of atoms; these groups of atoms are called functional groups.
Chemical properties involve one substance changing into another substance by reacting. An example of a chemical property is the ability of chlorine gas to react explosively when mixed with sodium. The chemical reaction creates a new substance, sodium chloride (table salt). Physical properties refer to different forms of a substance, but the substance remains the same; no chemical reaction or change to a new substance occurs.
Some of the properties that the functional groups provide include polarity and acidity. For example, the functional group called carboxyl (-COOH) is a weak acid. Polarity refers to one end of a molecule having a charge (polar), and the other end having no charge (nonpolar). For example, the plasma membrane has hydrophilic heads on the outside that are polar, and the hydrophobic tails (which are nonpolar) form the inside of the plasma membrane.
Periodic table of elements
If you’re studying organic chemistry, the periodic table is an important tool. The elements and their atomic numbers are listed and grouped together by their properties — making it easier to remember without having to memorize each element.
Important concepts of organic chemistry
When you’re studying organic chemistry, keep these helpful reminders close by because they highlight some of the most important concepts you’ll need to understand organic chemistry:
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Electronegativity increases as you go up and to the right in the periodic table.
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In reaction mechanisms, arrows show the movement of electrons; the tip of the arrow points to where the electrons are going.
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Resonance is a stabilizing feature of molecules; molecular stability generally increases as the number of resonance structures increases.
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Bronsted-Lowry acids are proton donors; Bronsted-Lowry bases are proton acceptors.
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Strong acids have weak (stable) conjugate bases.
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Conformation refers to the way a molecule folds itself in three-dimensional space based on the rotation around carbon-carbon single bonds; configuration (such as R or S configuration of a chiral center or cis or trans configuration of double bonds) refers to the specific orientation of atoms, which can change only through a chemical reaction.
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Only chiral molecules have enantiomers; enantiomers rotate plane-polarized light in equal and opposite directions.
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Molecules with chiral centers that have a plane of symmetry are called meso compounds; meso compounds are achiral.
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In order to have diastereomers, molecules generally have to have two or more chiral centers.
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Most organic reactions are driven by an electron-rich species (a nucleophile) attacking an electron-poor species (an electrophile).
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Double bonds are stabilized by alkyl substituents.
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Tertiary carbocations are more stable than secondary carbocations; secondary carbocations are more stable than primary carbocations. Allylic carbocations and benzylic carbocations are about as stable as secondary carbocations.
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Triple bonds are shorter than double bonds; double bonds are shorter than single bonds.
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Electrophiles are Lewis acids (electron acceptors); nucleophiles are Lewis bases (electron donors).
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Weak bases are good leaving groups; strong bases are bad leaving groups.
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Nucleophilicity generally parallels basicity. Typically, strong bases are also good nucleophiles.
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Primary halides undergo SN2 substitution; tertiary halides undergo SN1 substitution.
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Aromatics have 4n + 2 pi electrons; anti-aromatic compounds have 4n pi electrons.
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Substituents on aromatic rings with lone pairs on the ring-attaching atom are ortho-para directors.
