You are on page 1of 11

Biological Molecules Organic chemistry is the study of carbon compounds The study of carbon compounds, organic chemistry, focuses

on any compound with carbon (organic compounds). While the name, organic compounds, implies that these compounds can only come from biological processes, they can be synthesized by non-living reactions. Organic compounds can range from the simple (CO2 or CH4) to complex molecules, like proteins, that may weigh over 100,000 daltons. The overall percentages of the major elements of life (C, H, O, N, S, and P) are quite uniform from one organism to another. However, because of carbon’s versatility, these few elements can be combined to build an inexhaustible variety of organic molecules. While the percentages of major elements do not differ within or among species, variations in organic molecules can distinguish even between individuals of a single species. Carbon atoms are the most versatile building blocks of molecules With a total of 6 electrons, a carbon atom has 2 in the first shell and 4 in the second shell. Carbon has little tendency to form ionic bonds by losing or gaining 4 electrons. Instead, carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds. This tetravalence by carbon makes large, complex molecules possible. When carbon forms covalent bonds with four other atoms, they are arranged at the corners of an imaginary tetrahedron with bond angles near 109o. While drawn flat, they are actually three-dimensional. When two carbon atoms are joined by a double bond, all bonds around the carbons are in the same plane. They have a flat, three-dimensional structure. The electron configuration of carbon gives it compatibility to form covalent bonds with many different elements. The valences of carbon and its partners can be viewed as the building code that governs the architecture of organic molecules.

but butane has a straight skeleton and isobutane has a branched skeleton. it is possible to arrange the four groups in space in two different ways that are mirror images. Fats are biological molecules that have long hydrocarbon tails attached to a non-hydrocarbon component. Enantiomers are molecules that are mirror images of each other Enantiomers are possible if there are four different atoms or groups of atoms bonded to a carbon. Hydrocarbons are organic molecules that consist of only carbon and hydrogen atoms. butane and isobutane have the same molecular formula C4H10. The double bond does not allow atoms to rotate freely around the bond axis. The two butanes are structural isomers.Variation in carbon skeletons contributes to the diversity of organic molecules Carbon chains form the skeletons of most organic molecules. molecules with the same molecular formula but differ in the covalent arrangement of atoms. branched. Isomers are compounds that have the same molecular formula but different structures and therefore different chemical properties. . If this is true. The biochemistry of vision involves a light-induced change in the structure of rhodopsin in the retina from one geometric isomer to another. Petroleum is a fossil fuel because it consists of the partially decomposed remains of organisms that lived millions of years ago. Hydrocarbons are the major component of petroleum. or arranged in closed rings. Geometric isomers are compounds with the same covalent partnerships that differ in their spatial arrangement around a carbon-carbon double bond. The skeletons may vary in length and may be straight. The carbon skeletons may also include double bonds. For example.

The basic structure of testosterone (male hormone) and estradiol (female hormone) is identical. Each functional groups behaves consistently from one organic molecule to another. Functional groups are attachments that replace one or more hydrogen atoms to the carbon skeleton of the hydrocarbon. The L-Dopa isomer is an effective treatment of Parkinson’s disease. Functional groups contribute to the molecular diversity of life The components of organic molecules that are most commonly involved in chemical reactions are known as functional groups. but the D-Dopa isomer is inactive. Even the subtle structural differences in two enantiomers have important functional significance because of emergent properties from the specific arrangements of atoms. One enantiomer of the drug thalidomide reduced morning sickness. but the other isomer caused severe birth defects. There are six functional groups that are most important to the chemistry of life: hydroxyl. carboxyl. sulfhydryl. These then interact with different targets in the body. All are hydrophilic and increase solubility of organic compounds in water. the other inactive. The number and arrangement of functional groups help give each molecule its unique properties. its desired effect. amino. and phosphate groups.They are like left-handed and right-handed versions. carbonyl. Both are steroids with four fused carbon rings. Usually one is biologically active. but they differ in the functional groups attached to the rings. .

then the compound is a ketone. a hydrogen atom forms a polar covalent bond with an oxygen which forms a polar covalent bond to the carbon skeleton. Organic molecules with sulfhydryl groups are thiols. 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. A phosphate group (-OPO32-) consists of phosphorus bound to four oxygen atoms (three with single bonds and one with a double bond). Organic compounds with hydroxyl groups are alcohols and their names typically end in -ol. Sulfhydryl groups help stabilize the structure of proteins. have amino and carboxyl groups. A phosphate group connects to the carbon backbone via one of its oxygen atoms. . A sulfhydryl group (-SH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone. Organic compounds with amino groups are amines. the compound is an aldelhyde. If not. Amino acids.In a hydroxyl group (-OH). the building blocks of proteins. Isomers with aldehydes versus ketones have different properties. A carbonyl group (=CO) consists of an oxygen atom joined to the carbon skeleton by a double bond. This group resembles a hydroxyl group in shape. Compounds with carboxyl groups are carboxylic acids. The amino group acts as a base because ammonia can pick up a hydrogen ion (H+) from the solution. Because of these polar covalent bonds hydroxyl groups improve the solubility of organic molecules. If the carbonyl group is on the end of the skeleton. An amino group (-NH2) consists of a nitrogen atom attached to two hydrogen atoms and the carbon skeleton. A carboxyl group acts as an acid because the combined electronegativities of the two adjacent oxygen atoms increase the dissociation of hydrogen as an ion (H+). Phosphate groups are anions with two negative charges as two protons have dissociated from the oxygen atoms.

proteins. III Phosphate Methyl MACROMOLECULES: introduction Cells join smaller organic molecules together to form larger molecules. The chemical elements of life: a review Living matter consists mainly of carbon. hydrogen. Most macromolecules are polymers Three of the four classes of macromolecules form chainlike molecules called polymers. These elements are linked by strong covalent bonds. .One function of phosphate groups is to transfer energy between organic molecules. These larger molecules. macromolecules. II Carboxyl (Carboxylic acid) Amine or Amino Example Groups. and nucleic acids. 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. lipids. I Hydrogen Hydroxyl Example Groups. with smaller amounts of sulfur and phosphorus. oxygen. Polymers consist of many similar or identical building blocks linked by covalent bonds. Carbon with its four covalent bonds is the basic building block in molecular architecture.000 daltons. The four major classes of macromolecules are: carbohydrates. and nitrogen. may be composed of thousands of atoms and weigh over 100. Example Groups.

Hydrolysis reactions dominate the digestive process.The repeated units are small molecules called monomers. MACROMOLECULES CARBOHYDRATES 1 of 4 Classes Monosaccharides: “Mono-” means “one” Simple sugars — glucose. . This process requires energy and is aided by enzymes. fructose Usually with 5 or 6 carbons 5-carbon sugars are pentoses 6-carbon sugars are hexoses etc. guided by specific enzymes. Some monomers have other functions of their own. One monomer provides a hydroxyl group and the other provides a hydrogen and together these form water. Monomers are connected by covalent bonds via a condensation reaction or dehydration reaction. In hydrolysis as the covalent bond is broken a hydrogen atom and hydroxyl group from a split water molecule attaches where the covalent bond used to be. The covalent bonds connecting monomers in a polymer are disassembled by hydrolysis. The chemical mechanisms that cells use to make and break polymers are similar for all classes of macromolecules.

goes to other Digestion Dehydration / Hydrolysis Oligosaccharides “Oligo-” means “few” Few monosaccharides joined together Sucrose is disaccharide of glucose & fructose Often combined with other molecules Sometimes used for cell I.D. –OH. Plant Starch (Amylose) Starch Cellulose .Soluble in water Taste sweet Joining Builds bigger molecules H from one joins OH from another Forms water (condensation) Loose bonds of remaining molecules join Synthesis of starch Splitting Opposite of condensation "Splitting with water" Molecule broken in two Water is split (hydrolysis) –H+ goes to one.

Cellulose Structure & Function Chitin Like cellulose. but with nitrogenArthropods’ exoskeletons. vegetable oils. fungal cell walls Strong. mostly C & H Heterogeneous group Other classes more homogeneous Unified by insolubility in water Fatty-acid types: Oils & waxes Nonfatty-acid types: steroids Fat Molecules Triglycerides from beef.2nd of 4 Classes Slippery-oilies Nonpolar. Three fatty acids and a glycerol Glycerol has 3 carbons Each with an –OH group Each fatty acid has a COOH These condense to form triglyceride and H2O Fatty Acids Determines properties of fat Hydrocarbon chain with a COOH Most fats = 3 FAs + glycerol . and beer (makes bellies). very resistant to digestion Chitin Lipids .

No C=C double bonds Unsaturated .3rd of 4 Classes .One or more C=C double bonds Lipids Components of Triglycerides Triglyceride (Fat) Formation Beef Fat & Linseed Oil Phospholipids Phospholipids ..Glycerol: 3-carbon alcohol 3 OHs attract the COOH of FAs Saturated .mostly in membranes 1 glycerol. & 1 polar group Like a triglyceride. 1 FA swapped for polar group Soap-like properties Likes to get between polar and nonpolar materials Phospholipids Steroids Complex ring forms Some hormones Cholesterol Natural substance Found in membranes Athletes beware of androgenics! Steroids Proteins . 2 FAs..

vitamins and minerals to be healthy and shiny! It is a complex.build muscles and connective tissues! Amino Acids Small molecules — 20 kinds 1 amino group 1 carboxyl group 1 "R" group Joined by peptide bonds to form polypeptide Different sequence makes different protein Generic Amino Acid: 20 Different “R” Groups Structural Proteins HAIR--. Curling of Hair Peptide Bond Formation Peptide Bond: Phenylalanine-Leucine Dipeptide Levels of Protein Structure Like describing a knot by starting with the strands of the rope Primary: The sequence Secondary: Coiling of the chain Tertiary: Coiling of the coil .for digestion and food processing! Hormones.growth and homeostasis Structure.do they need vitamins? Hair is NOT alive and does not need proteins. highly organized compilation of dead cells forming strands….Proteins are amino acid polymers Many roles in cell Enzymes.

coiled to fit in small areas RNA: Manages synthesis Nucleotides 5-carbon sugar. a PO3. NAD) Some are chemical messengers (cAMP) Nucleotide Structure: 3 Parts Nucleic Acid Molecule Nucleotides can be joined together into a chain Cyclic AMP: (Adenosine Monophosphate) ATP: (Adenosine Triphosphate) Coenzyme Structure . and a nitrogenous base Not only serve to make RNA & DNA Some are energy carriers (ATP.Quaternary: Two or more chains together Illustration of Protein Structure Pleated Sheets Nucleic Acids: 4th of 4 Classes Nucleic acids are nucleotide polymers Genetics & cell control DNA: Genes.

%n°¾¾¾€f°– °f¯©°  nf °¾  ° f    °  € nf °–½¾°  ° € ¾  °  n¯½° ¾f°f   €°  ° n¯½° ¾f °  ¾¯ ¾f  ¾ ¾¾ ° ¾f  €€  °½½  ¾   nf –½% .

%n°¾¾¾€fnf °f¯f    ° f°– °f¯ f° f¾°–  ° f –½  .

¯½° ¾nf –½¾f nf nfn ¾  nf –½fn¾f¾f°fn  nf¾  n¯ °   n° –f ¾€ f ©fn °– ° f¯¾°n f¾   ¾¾nf°€ – °f¾f°°%+%   °f¯°–½% -%n°¾¾¾€f°– °f¯ffn  – °f¯¾f°   nf °¾  °  –f°nn¯½° ¾f¯°–½¾f f¯° ¾  @ f¯°–½fn¾f¾f f¾  nf¾ f¯¯°fnf°½n½f – °°%+%€¯ ¾°  ¯°fn ¾    °– n¾€½ °¾ f f¯°f° nf –½¾   ¾€ –½% %n°¾¾¾€f¾€f¯ ° f – °f¯f°   fn °  @¾–½ ¾ ¯  ¾f –½°¾f½  –f°n¯ n ¾¾€ –½¾f ¾  € –½¾ ½¾f   ¾n €½ °¾   ½¾½f –½% 9 %n°¾¾¾€½¾½¾ ° €– °f¯¾%  ¾°–  ° ¾f° ° f    ° %  ½¾½f –½n°° n¾ nf ° fn ° f° €¾– °f¯¾  9¾½f –½¾f f°°¾° –f nf– ¾f¾½°¾f  ¾¾nf €¯  – °f¯¾  .

° €°n°€½¾½f –½¾¾f°¾€  ° –  °–f°n¯ n ¾  @ n ¯nf  ¯ °¾€€ f   °–¯f n°¾¾¾¯f°€nf ° – °  – ° f° °– ° ¾¯f f¯°¾€ ¾€f° ½¾½¾  @ ¾   ¯ °¾f °  ¾°–nf ° ° ¾  .

f °¾€nf ° ° ¾¾  f¾n  °– n°¯ nffn n  @ – f  ¾€–f°n¯ n ¾ ¾½ nf½½  ¾ ¯ – €¯ °  ff°– ¯ °€ nf °¾  °f°  €°n°f–½¾ffn  ¾  °  f¯½ ½¾   – °   f¯½ ½¾  .

f %.

 .f nfn % ¯°  ¯° f¯½  ½¾  9¾½f  ..

..

D ° n° .

¾©°¾¯f –f°n¯ n ¾–  €¯f– ¯ n ¾  @ ¾ f– ¯ n ¾ ¯fn¯ n ¾ ¯f n¯½¾ €¾f° ¾€f¯¾f°  –    f°¾  @ €¯f©nf¾¾ ¾€¯fn¯ n ¾f nf  f ¾ ½ ¾ ½ °¾ f° °n nfn ¾  .¾¯fn¯ n ¾f ½¯ ¾ @ € €nf¾¾ ¾€¯fn¯ n ¾€¯nf° ¯ n ¾nf ½¯ ¾  9¯ ¾n°¾¾€¯f°¾¯f °nf  °– n¾°  nf ° ° ¾  .

.@  ½ f °¾f ¾¯f¯ n ¾nf ¯°¯ ¾  ¯ ¯°¯ ¾f  €°n°¾€ °   @ n ¯nf¯ nf°¾¯¾fn ¾¾ ¯f f°   f½¯ ¾f ¾¯f€fnf¾¾ ¾ €¯fn¯ n ¾   .°¯ ¾f n°° n  nf ° ° ¾ffn° °¾f° fn°  f°  fn°  ° ¯°¯ ½ ¾ f –½f°    ½ ¾f  – °f° –    ¾ €¯f   @¾½n ¾¾  ¾ ° –f° ¾f   °¯ ¾   @ nf ° ° ¾n°° n°–¯°¯ ¾°f½¯ f  ¾f¾¾ ¯    ¾¾  ° ¾¾f¾ nf ° ° ¾  °f – °f¯f°  –½€¯f¾½f  ¯ n ffn ¾   nf ° ° ¾    ¾¾ fn°¾ ¯°f   – ¾ ½n ¾¾  –  ¾½ n€n °¯ ¾  .

..

D .

 @€.

°¾fnnf ¾  #.° #¯ f°¾#° # ¯½ ¾–f¾ –n¾ €n¾  D¾fnf °¾  nf °¾–f¾f ½ °¾ ¾  nf °¾–f¾f  ¾ ¾ n  .f¾¾ ¾ .

  °f  @f¾ ¾  °°–  ¾ –– ¯ n ¾ €¯° ©°¾€¯f°  ¯¾f %n° °¾f°% ¾  ° ¾€ ¯f°°–¯ n ¾©° ° ¾¾€¾fn ½°– ½½¾ €n° °¾f° ½°–f   . n   °° Jf ¾¾½% ¾¾% +– ¾°   – ¾  – ¾°   f°$ ¾¾ –¾fnnf ¾ #– #¯ f°¾#€ #  ¯°¾fnnf ¾©° –   n¾ ¾ ¾fnnf €–n¾  €n¾  € °n¯ °  ¯ n ¾ ¯ ¯ ¾¾ €n    9f°fn%¯¾ % fn .

¾  .

.

¾  n  °n° .

°  n ¾  °– °  ½ ¾# ¾  °¾ €°–fn f¾ °–   ¾¾f° – ¾° .

° ½ ¾ ° €.

f¾¾ ¾ ½½   ¾ -°½f ¯¾.

 n ¾ @–n  ¾€¯ €  – f  ¾ f°  %¯f ¾  ¾%  @ €ffn ¾f° f–n  n f¾nf °¾ fnf° –½ fn€ffn f¾f.    – ° ¾–½  nf¾¾ ¾¯ ¯– ° ¾ D°€  °¾ °f  f fn ½ ¾ ¾ f ¾ -°€f fn ½ ¾ ¾  ¾ f.

 @ ¾ n° °¾ €¯–n  f°  fn ¾   ¯° ¾½½  ¾€€f  nf °nf°f.

 .¾€f¾ ¾+–n  .

n   nf °fn ¾ffn .

€¾ ff  -.

.

    ° ¾ D°¾ff  ° ¯ .

.

    ° ¾ ½ ¾ .

¯½° °¾€@–n  ¾ @–n   %f%¯f° €f °¾  9¾½½ ¾ 9¾½½ ¾ ¯¾°¯ ¯ f° ¾ –n  ¾  ½f–½  f–n   ¾f½½ €½f–½ f½  ½½  ¾  ¾–   °½ff° °°½f¯f f¾ 9¾½½ ¾   ¾ .

¯½ °–€¯¾ ¯ ¯° ¾ .

 ¾  -ff¾ ¾f°n  ° °¯ ¯ f° ¾   ¾ f €f° – °n¾"   ¾ 9 °¾  €.

f¾¾ ¾ .

9 °¾f f¯°fn ½¯ ¾ .f° ¾°n  °¯ ¾ € – ¾°f° € ½n ¾¾°–" ¯° ¾ –f° ¯ ¾f¾¾ n   ¯¾n ¾f° n°° n ¾¾ ¾" ¯°n ¾ ¯f¯ n ¾ ° ¾ f¯°–½ nf –½   –½ °  ½ ½  ° ¾€¯½½ ½  €€  °¾  °n ¯f ¾ €€  °½ °  ° n¯° n €€  °##½¾ nf9 °¾    ° f¯°¾" f¾-@f f°   ¾°° ½ °¾ f¯°¾f° ¯° f¾  ff° ¾°"¾f n¯½  ––f° n¯½f°€ f n ¾€¯°–¾f° ¾  .

°–€f 9 ½  ° ¯f° 9 ½  °  9 °ff°°  n° ½ ½    ¾€9 °n    ¾n °–f° ¾f°– ¾f° ¾€ ½  9¯f @ ¾  °n   n° f .

°–€ nf° @ f .

°–€ n .

.f °f @¯ nf°¾–   ¾f°€ 9 °n  9 f  ¾ -n nn ¾ €.

 n  -n  ¾nf° ©° –  °fnf° .9% -n   n 9f¾ -n nn .f¾¾ ¾ -n nfn ¾f °n  ½¯ ¾  ° n¾ n n° -  ° ¾ n €°¾¯ff f¾ - .f°f– ¾¾° ¾¾ -n  ¾  nf °¾–f f9 f° f°– °¾ f¾  -°¾  ¯f - - ¯ f  ° –nf ¾%@9 -% ¯ f n ¯nf¯ ¾¾ °– ¾%n.

°½¾½f % @9  % °¾° @½¾½f % .9  % °¾° .nn.

 °¯ n   .