Organic chemistry
Study of compounds containing carbon (originally defined as the chemistry of substances produced by living organisms but now extended to substances synthesized artificially). Originated in attempts to purify and improve the yield of other organisms as sou
Vitalism
Belief in a life force outside the jurisdiction of physical and chemical laws, crumbled after the laboratory synthesis of complex organic compounds.
Mechanism
Philosophical theory that all phenomena can be explained in terms of physical or biological causes.
Amino group (amines)
Chemical group consisting of a nitrogen atom bonded to two hydrogen atoms (-NH2); can act as a base in solution, accepting a hydrogen ion and acquiring a charge of 1+.
Example: Glycine
Ammonia
Small, very toxic molecule (NH3) produced by nitrogen fixation or as a metabolic waste product of protein and nucleic acid metabolism.
Carbonyl group (ketones and aldehydes)
Chemical group present in aldehydes (if located within the skeleton) and ketones (if located at the end of the skeleton) and consisting of a carbon atom double-bonded to an oxygen atom (>CO).
Ketones and aldehydes may be structural isomers. Ketones and al
Carboxyl group (carboxylic acid)
Chemical group present in organic acids and consisting of a single carbon atom double-bonded to an oxygen atom and also bonded to a hydroxyl group (-COOH). Can donate an H+ because of the polarity of the oxygen and hydrogen bond. Found ionized in cells.
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Enantiomer
Either one of a pair of compounds that are mirror images on each other, they differ in shape due to the presence of an asymmetric carbon, one that is attached to four different atoms of groups of atoms. Two enantiomers of a drug may not be equally effecti
Functional group
Specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and are usually directly involved in chemical reactions.
The most important chemical groups in biologic processes are 6 hydro philic functional groups (hydroxyl
Geometric isomer (cis-trans)
One of several compounds that have the same molecular formula and covalent arrangements but differ in the spatial arrangements of their atoms owing to the inflexibility of double bonds: single bonds allow the atoms they join to rotate freely about the bon
Hydrocarbon
Hydrophobic organic molecule consisting only of carbon and hydrogen. Major components of petroleum. Many cell's organic molecules have regions consisting of only carbon and hydrogen (i.e. fats have hydrocarbon tails). Most of the bonds are relatively non
Hydroxyl group (alcohol)
Chemical group consisting of an oxygen atom joined to a hydrogen atom (-OH). Polar (electrons spend more time near electronegative O). Can form hydrogen bonds with water molecules, helping dissolve organic compounds.
Example: ethanol.
Isomer
One of several compounds with the same molecular formula but different structures and therefore different properties. Usually only one isomer is biologically active because only that form can bind to specific molecules in an organism. The three types of i
Methyl group (methylated compounds)
Chemical group consisting of a carbon bonded to three hydrogen atoms (-CH3). The methyl group may be attached to a carbon or to a different atom. Can affect genetic expression and shape and function of sex hormones.
Example: 5-methyl cytedine.
Phosphate group (organic phosphates)
Chemical group consisting of a phosphorus atom bonded to four oxygen atoms (-OPO3 2-); potential to react with water to release energy. Contributes to negative charge to the molecule if located inside a chain of phosphates.
Example: glycerol phosphate.
Sulfhydryl group (thiols)
Chemical group consisting of a sulfur atom bonded to a hydrogen atom (-SH), similar shape to hydroxyl. Two sulfhydryls can form a covalent bond, this cross-linking stabilizes protein structures.
Example: cysteine.
Urea
Soluble nitrogenous waste produced in the liver by a metabolic cycle that combines ammonia with carbon dioxide.
Carbon as the backbone of life
- Carbon enters the biosphere through plants, they transform CO2 into the molecules of life, eaten by plant-eating animals
- Each atom of carbon has 4 valence electrons and act as an intersection point from which a molecule can branch off in as many as 4
Structural isomers
Isomers that differ in the covalent arrangements of their atoms. The number of possible isomers is correlated with the size of the carbon skeleton. These isomers may also differ in the location of double bonds.
Glycine
Compound that is both an amine and a carboxylic acid because it has both groups, and thus is called an amino acid.
Glycerol phosphate
Compound that provides the backbone for phospholipids. Most prevalent molecules in cell membranes, important for cell chemical reactions.
ATP (adenosine triphosphate)
Organic molecule formed by the link of adenosine and a strand of three phosphate groups. When ATP reacts with water, it releases energy used by the cell, one phosphate splits off and the molecule becomes ADP.