AP Biology Biochemistry: Carbon Carbon What is the valence number ? Organic Chemistry Branch of science dealing with the element carbon and its many properties. It is usually associated with all living organisms. About 30% of an organisms dry weight (called Biomass) is Carbon in organic molecules. Helps to make the organic molecules: Carbohydrates, Lipids, Proteins, and Nucleic Acids. The original source for Carbon in all life forms is Carbon Dioxide. (CO2)(Photosynthesis) Also supported by the Stanley Miller experiment, as discussed below. Stanley Miller Experiment (Took place in 1953.) He took inorganic substances found in Earths early atmosphere, such as H 2 O vapor, H 2, NH 3, CH 4, and created organic amino acids and oils. (CO 2 and CH 4 are not considered organic compounds, even though contain Carbon.) There are 20 amino acids that are used to make proteins in living organisms. Early Earth? (He analyzed volcanic gases to determine what the air must have been like.) Energy source to power the chemical reactions? (Electricity replaces lightning.) Stanley Miller LE 26-2 Water vapor CH 4 NH 3 H2H2 Electrode Condenser Cold water Cooled water containing organic molecules Sample for chemical analysis H2OH2O Early Earth Carbons e- configuration Carbon has versatility in four directions because of its Tetravalence. (Tetra means four) The tetravalence allows carbon to act like an intersection in the building of an organic molecule. This allows cells to build an almost infinite number of different molecules. Covalent bonding capabilities of Carbon Single Bond between Carbon atoms.(shown as: C-C) Double Bond between Carbon atoms. (shown as: C=C) Triple Bond between Carbon atoms. (shown as: C=C) . Carbon (valence = 4) SINGLE BONDS DOUBLE BONDS TRIPLE BONDS Carbon in a Tetrahedron! Has equidistant bond angles of 109.5. Carbon Bonding Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model Methane Ethane Ethene (ethylene) Hydrocarbons Molecules containing mostly Carbon and Hydrogen. Most hydrocarbons are energy sources. (Some examples are: Fossil fuels, Oils, And Fats) The more Hydrogen atoms in a molecule; the more energy there is in the molecule. Hydrocarbons are important parts of cell membranes. (The tails of phospholipids) All hydrocarbons are extremely hydrophobic because they are nonpolar molecules. (Afraid of waters polarity.) Hydrocarbon tails Hydrocarbon Tails of a Phospholipid Structural formula Space-filling model Phospholipid symbol Hydrophilic head Hydrophobic tails Fatty acids Choline Phosphate Glycerol Hydrophobic tails Hydrophilic head Cell Membranes Functional Groups Associated with Organic Molecules These are the sites of most organic molecules chemical reactions or properties. (They have a function to do.) Functional groups serve important purposes in molecules Estradiol Testosterone Male lion Female lion 7 functional groups are important in the chemistry of life (Pg. 64) Hydroxyl Carbonyl Carboxyl Amino Sulfhydryl Phosphate Methyl Hydroxyls (-OH) This group allows molecules to act as an alcohol or polar molecule. Name usually ends with ol. LE 4-10aa STRUCTURE (may be written HO) NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) Ethanol, the alcohol present in alcoholic beverages FUNCTIONAL PROPERTIES Is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3). Carbonyls (Only has one double bonded oxygen.) (It takes one stroke to make a lower case n.) Aldehydes (A is at one end of the alphabet.)(Carbonyl is located on the end of the molecule.) Ketones (K is in the middle of the alphabet.)(Carbonyl is located in the middle of the molecule.) LE 4-10ab STRUCTURE NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton EXAMPLE Acetone, the simplest ketone A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. Aldehydes if the carbonyl group is at the end of the carbon skeleton Acetone, the simplest ketone Propanal, an aldehyde FUNCTIONAL PROPERTIES Carboxyl (Has two oxygensone double bonded and one singled.)(It takes two strokes to make an x) These molecules can act as an acid by losing a Hydrogen atom and can also possibly polar too. LE 4-10ac STRUCTURE NAME OF COMPOUNDS Carboxylic acids, or organic acids EXAMPLE Has acidic properties because it is a source of hydrogen ions. Acetic acid, which gives vinegar its sour taste FUNCTIONAL PROPERTIES The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H + ) tend to dissociate reversibly; for example, Acetic acidAcetate ion In cells, found in the ionic form, which is called a carboxylate group. Amine (Contains Nitrogen) Can act as bases by picking up free H+. LE 4-10ba STRUCTURE NAME OF COMPOUNDS Amine EXAMPLE Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. FUNCTIONAL PROPERTIES Acts as a base; can pick up a proton from the surrounding solution: (nonionized) Ionized, with a charge of 1+, under cellular conditions Glycine (ionized) Sulfhydrls (Contains Sulfur) Sulfur can make Di-Sulfide bridges for pockets in protein formation. LE 4-10bb STRUCTURE (may be written HS) NAME OF COMPOUNDS Thiols EXAMPLE Ethanethiol FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20). Phosphate ( Contains Phosphorus) These molecules are usually involved in E Transfers, such as associated with ATP. It can also act like an Anion, a negative ion. LE 4-10bc STRUCTURE NAME OF COMPOUNDS Organic phosphates EXAMPLE Glycerol phosphate FUNCTIONAL PROPERTIES Makes the molecule of which it is a part an anion (negatively charged ion). Can transfer energy between organic molecules. Methyl