Carbon+and+Macromolecules

=__Carbon and Macromolecules__= //by Hilary Langley//

All images provided by //Google Images//

__Vocabulary:__

 * //organic chemistry:// the branch of chemistry that specializes in the study of carbon compounds
 * //hydrocarbons:// organic molecules consisting only of carbon and hydrogen
 * //isomers:// compounds that have the same molecular formula but different structures and different properties
 * //structural isomers:// differ in the covalent arrangements of their atoms
 * //geometric isomers:// have all the same covalent partnerships, but they differ in spatial arrangements
 * //enantiomers:// molecules that are mirror images of each other
 * //functional groups:// components of organic molecules that are most commonly involved in chemical reactions
 * //hydroxyl group// a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule.
 * //alcohols:// organic compounds containing //hydroxyl groups//
 * //carbonyl group:// consists of a carbon atom joined to an oxygen atom by a double bond
 * //aldehyde:// type of organic compound if the //carbonyl group// is on the end of a carbon skeleton
 * //ketone:// type of organic compound if the //carbonyl group// is __not__ on the end of a carbon skeleton
 * //carboxyl group:// the name of the entire assembly of atoms when an oxygen atom is double-bonded to a carbon atom that is also bonded to a hydroxyl group
 * //carboxylic acids (organic acids):// atoms containing //carboxyl groups//
 * //amino group:// consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton
 * //amines:// organic compounds containing //amino groups//
 * //sulfhydryl group:// consists of a sulfur atom bonded to an atom of hydrogen (resembles a //hydroxyl group// in shape)
 * //thiols:// organic compounds containing //sulfhydryl groups//
 * //phosphate group:// have a phosphate ion covalently attached by one of its oxygen atoms to a carbon skeleton

__Important Content:__
- __**Objective 1:**__ //Organic chemistry is the study of carbon compounds//
 * Compounds containing carbon are organic compounds. The branch of chemistry that specializes in the study of these compounds is called //organic chemistry.// Organic compounds vary from such things as simple molecules like methane (CH 4) to very large molecules like proteins with thousands of atoms.
 * Major elements of life:
 * Carbon (C)
 * Hydrogen (H)
 * Oxygen (O)
 * Nitrogen (N)
 * Sulfur (S)
 * Phosphorus (P)
 * Organic chemistry began with attempts to purify and improve the yield of valuable substances (food, medicine, etc). In the 19th century scientists were able to construct many simple compounds in the laboratory. Doing this with larger and complex molecules seemed impossible.
 * Swedish chemist Berzelius made the first distinction between organic compounds (those that could arise within only living organisms) and inorganic compounds (those that were found in the nonliving world).
 * Chemists brought the abiotic synthesis process and related it to evolution. Stanley Miller used a laboratory simulation of the chemical conditions of primitive Earth to show that the spontaneous synthesis of organic compounds could have been an early stage of life.

- __**Objective 2:**__ //Carbon atoms are the most versatile building blocks of molecules//


 * Carbon has 6 electrons (e-). Two in the first electron shell, and for in the second shell. Having four valence electrons in a shell that holds eight means that carbon has a little tendency to gain or lose e- and form ionic bonds. To do so, four e- would need to be gained or lost. Instead of gaining or losing e-, carbon usually shares e- with other atoms through covalent bonds.
 * When a carbon atom forms single covalent bonds the arrangement of it's four hybrid orbitals causes the bonds to angle themselves around an imaginary tetrahedron.
 * Molecules are three dimensional and their shape often determines their function.
 * Carbon's electron configuration makes it covalently compatible with many different elements.
 * EXAMPLES OF CARBON'S COVALENT BONDS:
 * Methane
 * CO2

- __**Objective 3:**__ //Variation in carbon skeleton contributes to the diversity of organic molecules//
 * Carbon chains form the skeletons of most organic molecules. They vary in length and can be straight, branched, or arranged in closed rings.
 * //Hydrocarbons// are organic molecules consisting only of carbon and hydrogen
 * Examples of //hydrocarbons//
 * //Isomer tree://

//(Definitions and explanations of each type of isomer in the vocabulary section).//

- __**Objective 4:**__ //Functional groups also contribute to the molecular diversity of life//
 * Functional groups can be viewed as attachments that can replace one or more of the hydrogens bonded to the carbon skeleton of the hydrocarbon.
 * However, some functional groups include atoms of the carbon skeleton as well.
 * Each group behaves consistently from one organic molecule to another, and the number and arrangement of the groups help give each molecule its unique properties.
 * There are six functional groups that are most important in the world of chemistry
 * The Hydroxyl Group
 * See vocabulary definition
 * [[image:http://trc.ucdavis.edu/biosci10v/bis10v/week2/2webimages/Groups_5.gif width="337" height="336" align="right"]]The names of the alcohols usually end in -ol (ex: ethanol)
 * Usually abbreviated by omission of the covalent bond between oxygen and hydrogen (-OH or HO-)
 * The hydroxyl group is polar because of the electronegative oxygen atom drawing e- toward itself
 * Water molecules are attracted to the hydroxyl group
 * Sugars owe their solubility in water to the hydroxyl group
 * The Carbonyl Group
 * See vocabulary definition
 * If placed on the end of a carbon skeleton the organic compound is called an aldehyde
 * If not placed on end of a carbon skeleton then the organic compound is called a ketone
 * The simplest ketone is acetone
 * The Carboxyl Group
 * See vocabulary definition
 * The simplest one-carbon compound called formic acid (HCOOH), is the substance some ants inject when they sting
 * Acetic acid (two-carbon compound) gives vinegar its sour taste
 * In general, acids are sour
 * The covalent bond between the oxygen and the hydrogen is so polar that the hydrogen tends dissociate reversibly from the molecule as an ion.
 * The Amino Group
 * Ex: Glycine (also has a carboxyl group)
 * Acts as a base
 * Have a charge of +1
 * The Sulfhydryl Group
 * See vocabulary definition/explanation
 * The Phosphate group
 * See vocabulary definition
 * Loss of hydrogen ions by dissociation leaves phosphate with a negative charge
 * One function is the transfer of energy between organic molecules

- __**Objective 5:**__ //The Chemical Elements of Life : A Review//
 * Living matter is made mostly of carbon (C), oxygen (O), hydrogen (H), and nitrogen (N), with some sulfur (S), and phosphorus (P)

__Related links for further information:__

 * [|Wikipedia - Organic Chemistry]
 * [|organic-chemistry.org]
 * [|CHEMystery- Organic Chemistry]
 * [|Science News - Organic Chemistry]

__Vocabulary:__

 * //Polymer:// a long molecule consisting of many identical or similar building blocks linked by covalent bonds, much as a train consists of a chain of cars
 * //Monomer:// the repeating units (small molecules) that serve as building blocks of //polymers//
 * //Condensation reaction:// Monomers are connected by a reaction in which two molecules are covalently bonded to each other through the loss of a water molecule (specifically a //dehydration reaction// because water is lost).
 * //Hydrolysis:// a process that is essentially the reverse of the //dehydration reaction//
 * //Carbohydrates:// includes both sugars and their //polymers//
 * //Monosaccharides:// single sugars
 * //Disaccharide:// consists of two //monosaccharides//
 * //Glycosidic linkage:// a covalent bond formed between two //monosaccharides// by a //dehydration reaction//
 * //Polysaccharides:// macromolecules, //polymers// with a few hundred to a few thousand //monosaccharides// joined by //glycosidic linkages//
 * //Starch:// a storage //polysaccharide// of plants, consisting entirely of glucose //monomers//
 * //Chitin:// structural //polysaccharide// used by arthropods
 * //Lipids:// one class of large biological molecules that doesn't include //polymers//; hydrophobic; consist mos[[image:http://www.virtualsciencefair.org/2004/thog4n0/public_html/fatyacid.jpg align="right"]]tly of hydrocarbons
 * //Fat:// constructed from glycerol and //fatty acids//
 * //Fatty Acid:// has a long carbon skeleton, usually 16 or 18 carbon atoms in length
 * //Triacylglycerol:// consists of three //fatty acids// linked to one glycerol molecule
 * //Saturated fatty acid:// present when no double bonds occur between carbon atoms composing the tail, then as many hydrogen atoms as possible are bonded to the carbon skeleton
 * //Unsaturated fatty acid:// has one or more double bonds, formed by the removal of hydrogen atoms from the carbon skeleton
 * //Phospholipids:// similar to fats, but with only two //fatty acids// instead of three
 * //Steroids:// lipids characterized by a carbon skeleton consisting of four fused rings
 * //Cholesterol:// a common component of animal cell membranes and is also the precursor from which other steroids are synthesized
 * //Proteins:// used for structural support, storage, transport of other substances, signaling from one part of the organism to another, movement, and defense against foreign substances[[image:http://homepages.ius.edu/GKIRCHNE/peptide.jpg width="370" height="294" align="right"]]
 * //Conformation:// each //protein's// unique three-dimensional shape
 * //Polypeptides:// polymers of //amino acids//
 * //Amino acids:// organic molecules possessing both carboxyl and amino groups
 * //Peptide bond:// the resulting covalent bond from a //dehydration reaction//
 * //Primary structure//: a //protein's// unique sequence of //amino acids//
 * //Secondary sequence:// the coils and folds of a //polypeptide// chain
 * //Alpha helix:// a secondary structure; a delicate coil held together by hydrogen bonding between every fourth //amino acid//
 * //Pleated sheet:// a secondary structure; two regions of the //polypeptide// chain lie parallel to each other
 * //Tertiary structure:// consisting of irregular contortions from bonding between side chains of the various //amino acids//
 * //Hydrophobic interaction:// as a //polypeptide// folds into its functional //conformation//, //amino acids// with hydrophobic (nonpolar) side chains usually congregate in clusters at the core of the protein, out of contact with water
 * //Disulfide bridges:// form where two cysteine //monomers//, //amino acids// with sulfhydryl groups (-SH) on their side chains, are brought close together by the folding of the protein
 * //Quaternary structure:// the overall protein structure that results from the aggregation of these //polypeptide// subunits
 * //Denaturation:// a change which occurs if the pH, [salt], temperature, or other aspects of a //protein's// en[[image:http://fig.cox.miami.edu/~cmallery/255/255prot/gk2x43.gif width="329" height="353" align="right"]]vironment are altered, it may unravel and lose its native //conformation//
 * //Nucleotides:// //monomers// of nucleic acids
 * //Pyrimidine:// has a six-membered ring of carbon
 * //Double helix:// the DNA molecules of cells consist of two polynucleotides that spiral around an imaginary axis
 * //Double helix:// the DNA molecules of cells consist of two polynucleotides that spiral around an imaginary axis

__Important Content:__

 * -** __**Objective 1:**__ //Most macromolecules are polymers//
 * See vocabulary definitions
 * Carbohydrates, lipids, proteins, and nucleic acids are the four major classes of organic compounds in cells.
 * Some of the compounds are extremely large (called macromolecules)
 * Most of these large macromolecules are polymers (chains of monomers)
 * These monomers form larger molecules by condensation reactions in which water molecules are released, called dehydration.
 * Polymers can disassemble by a reverse process, called hydrolysis

- __**Objective 2:**__ //An immense variety of polymers can be built from a small set of monomers//
 * See vocabulary definitions
 * Each polymer class is formed by a certain number of monomers
 * Organisms share the same limited number of monomer types, each organism is different and unique because of the arrangement of the monomers into polymers

- __**Objective 3:**__ //Sugars, the smallest carbohydrates, serve as fuel and carbon sources//
 * See vocabulary definitions
 * Monosaccharides are the simplest form of sugars
 * They are used for direct fuel/energy, converted into other types of organic molecules, or used as monomers for polymers.
 * Disaccharides = 2 monosaccharides connected by a glycosidic linkage

- __**Objective 4:**__ //Polysaccharides, the polymers of sugars, have storage and structural roles//
 * See vocabulary definitions
 * Starch (plants) and glycogen (animals) are storage polymers
 * Cellulose is an important structural polymer of glucose in plant cell walls
 * They differ in the positions and orientations of the glycosidic linkages

- __**Objective 5:**__ //Fats store large amounts of energy//
 * See vocab definitions
 * Fats are constructed by joining a glycerol molecule to three fatty acids by dehydration reactions
 * Saturated fatty acids have the maximum number of hydrogen atoms
 * Unsaturated fatty acids (oils) have one or more double bonds between carbons

- __**Objective 6:**__ //Phospholipids are major components of cell membranes//
 * See vocabulary definitions/explanations
 * Phospholipids have a negatively charged phosphate group which may be joined to another small hydrophilic molecule

- __**Objective 7:**__ //Steroids include cholesterol and certain hormones//
 * See vocabulary definitions
 * Steroids have a basic structure of four fused rings of carbon atoms
 * Many hormones including vertebrate sex hormones are steroids produced from cholesterol

- __**Objective 8:**__ //A polypeptide is a polymer of amino acids connected in specific sequence//
 * See vocabulary definitions
 * Proteins are constructed from 20 different amino acids, each with a characteristic side chain (R group)
 * Carboxyl and amino groups of adjacent amino acids will link together through peptide bonds

- __**Objective 9:**__ //A protein's function depends on its specific conformation// - __**Objective 10:**__ //Nucleic acids store and transmit hereditary information//
 * See vocabulary definitions
 * The primary structure of a protein is its sequence of amino acids
 * The secondary structure is the folding or coiling of polypeptide into structures like the alpha helix or the pleated sheet.
 * These result from hydrogen bonding between the parts of the polypeptide backbone
 * Tertiary structure is the overall three-dimensional shape of a polypeptide (results from interactions between amino acid side chains)
 * Proteins with more than one polypeptide chain have a quaternary level of structure.
 * The structure and function of a protein are sensitive to both the surrounding chemical and physical conditions. [[image:http://www.contexo.info/DNA_Basics/images/proteinstructuresweb.gif align="center"]]
 * DNA stores information for protein synthesis
 * RNA carries this genetic information to the protein-synthesizing machinery

- **__Objective 11:__** //A nucleic strand is a polymer of nucleotides//
 * See vocabulary definitions
 * Each nucleotide monomer contains a pentose covalently bonded to a phosphate group and to one of four different nitrogen bases (A, C, G, and T or U)
 * RNA -
 * has ribose as its pentose
 * has U[[image:http://tigger.uic.edu/classes/phys/phys461/phys450/ANJUM04/RNA_sstrand.jpg width="435" height="468" align="center"]]
 * DNA -
 * has deoxyribose as its pentose
 * has T[[image:http://academic.brooklyn.cuny.edu/biology/bio4fv/page/molecular%20biology/16-05-doublehelix.jpg align="center"]]
 * Nucleotides join to a sugar-phosphate backbone from which the nitrogen bases project, to form a polynucleotide
 * The sequence of the bases along a gene specifies which protein is to be synthesized.

- __**Objective 12:**__ //Inheritance is based on replication of the DNA double helix//
 * See vocabulary definitions
 * DNA is a helical, double-stranded macromolecule with bases projecting into the interior of the molecule
 * A always bonds to T, and C always bonds to G, the nucleotides are complementary to one another, one strand can serve as a template for the other strand
 * This provides a mechanism for the continuity of life

- __**Objective 13:**__ //We can use DNA and proteins as tape measures of evolution//
 * Molecular comparisons help biologists sort out the evolutionary connections among species

Related links for further information:

 * [|Wikipedia - Macromolecules]
 * [|Easy Lab - Test for organic molecules]
 * [|Organic Molecules]