Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Organic Chemistry (Carbon Chemistry) Vitalism, the idea that organic compounds arise only in organisms, was disproved when chemists synthesized these compounds © 2011 Pearson Education, Inc. Stanley Miller’s classic experiment demonstrated the abiotic synthesis of organic compounds Experiments support the idea that abiotic synthesis of organic compounds, perhaps near volcanoes, could have been a stage in the origin of life © 2011 Pearson Education, Inc. EXPERIMENT “Atmosphere” CH4 Water vapor Electrode Condenser Cooled “rain” containing organic molecules H2O “sea” Sample for chemical analysis Cold water Carbon chemistry Organic molecules contain carbon Atomic number is 6 Carbon has a valence of 4 It can form 4 covalent bonds(tetravalence ) 4 covalent CARBON bonds form a shape called TETRAHEDRON Tetrahedron modified from: http://faculty.uca.edu/~johnc/mole1440.htm Images from: http://www.school-for-champions.com/science/chemhydrocarbon.htm TETRAVALENCE makes large complex molecules with a variety of shapes possible http://nrr.georgetown.edu/NRR/struc,actv.html Organic molecules can take on many shapes: A. branches B. chains C. rings These covalent bonds are energy-rich!! Hydrocarbons are the major component of propane and gasoline!! Butane Isobutane Hexane Cyclohexane Ethane Methane Ethene Fats are biological molecules that have long hydrocarbon tails attached to a non-hydrocarbon component. Nucleus Fat droplets 10 m (a) Part of a human adipose cell (b) A fat molecule Isomers are compounds that have the same molecular formula but different structures and therefore different chemical properties. The L-Dopa isomer is an effective treatment of Parkinson’s disease, but the D-Dopa isomer is inactive. Enantiomers are molecules that are mirror images of each other Drug Condition Ibuprofen Pain; inflammation Albuterol Effective Enantiomer Ineffective Enantiomer S-Ibuprofen R-Ibuprofen R-Albuterol S-Albuterol Asthma Organic molecules are most important to the chemistry of life! Organic molecules are dependent upon: The arrangement of the carbon skeleton The components that are attached to the carbon skeleton The components attached to the carbon skeleton are called functional groups The functional groups are often involved in chemical reactions Functional groups have unique properties The basic structure of testosterone (male hormone) and estradiol (female hormone) is identical. ▪ Both are steroids with four fused carbon rings, but they differ in the functional groups attached to the rings. The seven functional groups that are most important in the chemistry of life: Hydroxyl group Carbonyl group Carboxyl group Amino group Sulfhydryl group Phosphate group Methyl group Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Hydroxyl Group (-OH) Ex: alcohols polar (oxygen); Helps dissolve organic compounds Names typically end in -ol Ex: Ethanol Carbonyl Group(=CO) KETONE: within carbon skeleton ALDEHYDE: at end of carbon skeleton GLUCOSE FRUCTOSE http://61039206.sinagirl.com/carbohydate.JPG http://web1.caryacademy.org/chemistry/rushin/StudentProjects/CompoundWebSites/1999/Sucrose/sucrose_structure.gif Carboxyl Group(-COOH) Ex: carboxylic acids organic acids acidic http://dl.clackamas.cc.or.us/ch106-05/common.htm Amino Group (–NH2) Called: amines Ex: amino acids (glyceine) (have both amino & carboxyl groups) Basic Amino Group Can act as a base and pick up a H+ ion Carboxyl Group can act as an acid and give up a H+ ion H | R -C -COO| +NH3 Sulfhydral Group (-SH) Called: thiols Example: Cycteine (AA) http://www.mun.ca/biology/scarr/Disulfide_bridge.htm Disulfide bridges stabilize protein structure http://www.britannica.com/ebc/art-3207/Conformation-of-lysozyme LYSOZYME Phosphate Group (-OPO3 or –PO4) Organic phosphates Glycerol backbone of phospholipids Makes molecule negatively charged Can store & transfer energy ~ ATP METHYL Group (-CH3) Makes molecule more NON-POLAR Methylated compounds METHYLATION: Adding methyl groups to DNA “turns off” genes http://students.cis.uab.edu/rmeghana/methylation.html CHEMICAL GROUP Hydroxyl Carbonyl Carboxyl STRUCTURE (may be written HO—) NAME OF COMPOUND In a hydroxyl group (—OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–.) The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond. When an oxygen atom is double-bonded to a carbon atom that is also bonded to an —OH group, the entire assembly of atoms is called a carboxyl group (—COOH). Alcohols (their specific names usually end in -ol) Ketones if the carbonyl group is within a carbon skeleton Carboxylic acids, or organic acids Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE Ethanol, the alcohol present in alcoholic beverages Acetone, the simplest ketone Acetic acid, which gives vinegar its sour taste Propanal, an aldehyde FUNCTIONAL PROPERTIES Is polar as a result of the electrons spending more time near the electronegative oxygen atom. A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars. These two groups are also found in sugars, giving rise to two major groups of sugars: aldoses (containing an aldehyde) and ketoses (containing a ketone). Has acidic properties because the covalent bond between oxygen and hydrogen is so polar; for example, Acetic acid Acetate ion Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion). In a hydroxyl group (-OH), a hydrogen atom forms a polar covalent bond with an oxygen which forms a polar covalent bond to the carbon skeleton. Organic compounds with hydroxyl groups are alcohols and their names typically end in -ol. A carbonyl group (=CO) consists of an oxygen atom joined to the carbon skeleton by a double bond. If the carbonyl group is on the end of the skeleton, the compound is an aldelhyde. If not, then the compound is a ketone. Carboxyl STRUCTURE Carboxylic acids, or organic acids EXAMPLE Has acidic properties because the covalent bond between oxygen and hydrogen is so polar; for example, Acetic acid, which gives vinegar its sour taste Acetic acid Acetate ion Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion). NAME OF COMPOUND FUNCTIONAL PROPERTIES A carboxyl group (-COOH) consists of a carbon atom with a double bond with an oxygen atom and a single bond to a hydroxyl group. Compounds with carboxyl groups are carboxylic acids. Amino STRUCTURE NAME OF COMPOUND Amines EXAMPLE Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms). Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions. FUNCTIONAL PROPERTIES An amino group (-NH2) consists of a nitrogen atom attached to two hydrogen atoms and the carbon skeleton. Organic compounds with amino groups are amines. The amino group acts as a base because ammonia can pick up a hydrogen ion (H+) from the solution. Amino acids, the building blocks of proteins, have amino and carboxyl groups. Phosphate STRUCTURE Organic phosphates EXAMPLE Glycerol phosphate In addition to taking part in many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes. Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates). Has the potential to react with water, releasing energy. NAME OF COMPOUND FUNCTIONAL PROPERTIES A phosphate group (-OPO32-) consists of phosphorus bound to four oxygen atoms Sulfhydryl STRUCTURE Thiols NAME OF COMPOUND (may be written HS—) EXAMPLE Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. Cysteine Cysteine is an important sulfur-containing amino acid. Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breaking and re-forming the cross-linking bonds. FUNCTIONAL PROPERTIES A sulfhydryl group (-SH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone. Sulfhydryl groups help stabilize the structure of proteins. Methyl STRUCTURE Methylated compounds EXAMPLE Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes. 5-Methyl cytidine 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group. Arrangement of methyl groups in male and female sex hormones affects their shape and function. NAME OF COMPOUND FUNCTIONAL PROPERTIES 1. Living matter consists mainly of carbon, oxygen, hydrogen, and nitrogen, with smaller amounts of sulfur and phosphorus. 2. These elements are linked by strong covalent bonds. 3. Carbon with its four covalent bonds is the basic building block in molecular architecture. 4. The great diversity of organic molecules with their special properties emerge from the unique arrangement of the carbon skeleton and the functional groups attached to the skeleton. 1. 2. 3. Explain how carbon’s electron configuration explains its ability to form large, complex, diverse organic molecules Describe how carbon skeletons may vary and explain how this variation contributes to the diversity and complexity of organic molecules Distinguish among the three types of isomers: structural, geometric, and enantiomer Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 4. 5. Name the major functional groups found in organic molecules; describe the basic structure of each functional group and outline the chemical properties of the organic molecules in which they occur Explain how ATP functions as the primary energy transfer molecule in living cells Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings