Chapter 4: Carbon and the Molecular Diversity of Life AP Biology
Overview: Carbon: The Backbone of Life Even though water is the universal medium for life on Earth, living organisms are made mostly of the element carbon Carbon enters biosphere through action of plants During photosynthesis, they use solar energy to transform CO 2 in atmosphere into molecules needed for life (glucose and other related organic compounds) These molecules are then passed along to animals that feed on plants Of all the chemical elements, carbon is unparalleled in its ability to form molecules that are large, complex, and diverse This molecular diversity has made possible the diversity of organisms that have evolved on Earth Molecules that distinguish living from nonliving matter (like proteins, DNA, carbohydrates) are all composed of carbon atoms bonded to one another and to atoms of other elements (often H, O, N, S, and P)
Concept 4.1: Organic chemistry is the study of carbon compounds
The branch of chemistry that specializes in the study of carbon compounds is called ORGANIC CHEMISTRY Organic compounds range from simple molecules (ex: methane CH 4 ) to very large one made up of 1000s of atoms (proteins) Most organic compounds contain hydrogen atoms in addition to carbon atoms The overall percentages of the major elements of life (C, H, N, S, P) are fairly constant from one organism to another, However, they can be used to build an almost inexhaustible variety of organic molecules by assorting them in different ways Different species of organisms and different individuals within a species are distinguished in this way by variations in their organic molecules
The science of organic chemistry originated in the attempt to purify and improve the yield of valued substances (food, medicine, fabrics) obtained from living organisms By the early 1800s, chemists had learned to make many simple compounds in the lab by combining elements under the right conditions Scientists at this time, however, believed that artificial synthesis of complex molecules found in living matter was impossible This belief, that organic compounds could arise only in organisms, was called VITALISM Chemists began to chip away at the foundation of vitalism when they finally learned to synthesize organic compounds in labs Urea, an organic compound present in the urine of mammals, was one of the first organic compounds to be artificially made in 1928 The synthesis of urea occurred accidentally, while German chemist Friedrich Wohler was attempting to make an inorganic salt called ammonium cyanate by mixing ammonium and cyanate ions (created urea instead) Because one of the ingredients used in the synthesis (cyanate) had been extracted from animal blood, however, many vitalists were still not swayed by Wohler s discovery
Vitalism crumbled completely after several decades of artificial synthesis of increasingly complex organic compounds One of these experiments included Stanley Miller s synthesis of organic compounds related to evolution Miller s experiment tested whether complex organic molecules could arise spontaneously under conditions thought to have existed on early Earth (see next slide) These pioneers of organic chemistry helped shift mainstream biological thought from vitalism to MECHANISM Mechanism is the view that physical and chemical laws govern all natural phenomena, including the processes of life Organic chemistry was thus redefined as the study of carbon compounds, regardless of origin
Experiment: In 1953, Stanley Miller set up a closed system to simulate conditions thought to have existed on early Earth 1) Water mixture in sea flask was heated; vapor entered atmosphere flask 2) Atmosphere flask contained mix of hydrogen gas, methane, ammonia, and water vapor (believed to mimic early Earth s atmosphere) 3) Sparks were discharged to mimic lightning 4) Condenser cooled the atmosphere, raining water and any dissolved molecules down into sea flask 5)As material cycled through apparatus, Miller periodically collected samples for analysis Results: Miller identified variety of organic molecules common in organisms (including simple molecules like formaldehyde (CH 2 O) and hydrogen cyanide (HCN) and more complex molecules (like amino acids and hydrocarbons) Conclusion: Organic molecules (a 1 st step in the origin of life) may have been synthesized abiotically on early Earth
Concept Check 4.1 1) What conclusion did Stanley Miller draw when he found amino acids in the products of his experiment? 2) When Miller tried the experiment in Figure 4.2 (pp. 59) without the electrical discharge, no organic compounds were found. What might explain this result?
Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms
Electron configuration is the key to an atom s characteristics Electron configuration determines: The kinds of bonds an atom will form with other atoms The number of bonds an atom will form with other atoms
The Formation of Bonds with Carbon Carbon has 6 electrons (2 electrons in the 1 st shell; 4 valence electrons in the 2 nd shell, which can hold up to 8) Carbon would have to either donate or accept 4 electrons to complete its valence shell and become an ion Instead, carbon usually completes its valence shell by sharing its 4 electrons with other atoms in covalent bonds so that 8 electrons are present This characteristic is called TETRAVALENCE
The Formation of Bonds with Carbon Carbon may form bonds that are single or double covalent bonds: When carbon atom forms 4 single covalent bonds, the arrangement of its 4 hybrid orbitals causes bonds to angle toward corners of an imaginary tetrahedron (roughly 109.5 degrees) When 2 carbon atoms are joined by a double bond, all bonds around those carbons are in the same plane, giving the molecule a flat shape
The electron configuration of carbon gives it covalent compatibility with many different elements The valences of carbon, along with its most frequent partners (O,H,N) are the basis for the rules of covalent bonding in organic chemistry We can think of it as the building code for the architecture of organic molecules Recall: Valence is the number of covalent bonds an atom can form It is usually equal to the number of electrons required to complete the valence (outermost) shell All the electrons are shown for each atom in the electron distribution diagrams (above) Only the electrons in the valence shell are presented in the Lewis dot structure of each atom (below)
Let s consider how rules of covalent bonding apply to carbon atoms with partners other than hydrogen: Ex) CO 2 a single carbon atom is joined to 2 atoms of oxygen by double covalent bonds Each line in its structural formula represents a pair of shared electrons Carbon (6) has 4 valence electrons and can thus form 4 bonds to fill valence shell Oxygen (8) has 6 valence electrons and thus can form 2 bonds to fill valence shell The 2 double bonds are equivalent to 4 single covalent bonds (This arrangement therefore completes the valence shells of all atoms in the molecule) O = C = O
Let s consider how rules of covalent bonding apply to carbon atoms with partners other than hydrogen: Ex) Urea organic compound found in urine that Wohler synthesized in early 1880s Molecular formula: CO(NH 2 ) 2 Nitrogen (7) has 5 valence electron and can thus form 3 bonds to fill valence shell Carbon again can form 4 bonds Oxygen can again form 2 bonds
Molecular Diversity Arising from Carbon Skeleton Variation Carbon chains form the skeletons of most organic molecules Skeletons can vary in length and shape Shapes can include (1) straight, (2) branched, and (3) arranged in closed rings Some skeletons can also include double bonds, which vary in location and number This variation in carbon skeletons is one important source of molecular complexity and diversity that characterizes living matter In addition, even more variation is added to these carbon skeletons when we consider atoms of other elements that can be bonded to the skeletons at available sites Animation: Carbon Skeletons
Hydrocarbons HYDROCARBONS organic molecules consisting of only carbon and hydrogen Atoms of hydrogen are attached to carbon skeleton wherever electrons are available for covalent bonding Hydrocarbons are very common on Earth Hydrocarbons are major components of petroleum Petroleum is called a FOSSIL FUEL because it consists of partially decomposed remains of organisms that lived millions of years ago Many of the cell s organic molecules have regions consisting only of hydrocarbons Ex) Fats have long hydrocarbon tails attached to a non-hydrocarbon component
Hydrocarbons Characteristics of Hydrocarbons: Hydrocarbons are relatively NONPOLAR and thus DO NOT DISSOLVE in water Hydrocarbons can UNDERGO REACTIONS that release relatively large amounts of energy Gas that fuels cars consists of hydrocarbons Hydrocarbon tails of fat molecules serve as stored fuel for animal bodies
Isomers Variation in the architecture of organic molecules can be seen in isomers: Isomers: compounds that have the same number of atoms of the same elements but different structures and hence different properties 1) Structural isomers: differ in covalent arrangements of their atoms 2) Geometric isomers: have same covalent partnerships but differ in spatial arrangement 3) Enantiomers: isomers that are mirror images of each other Animation: Isomers
Structural Isomers 1) Structural isomers: differ in covalent arrangements of their atoms The number of possible isomers increases with increasing size of carbon skeleton Ex) C 5 H 12 3 isomers (2 shown here) Ex) C 8 H 18 18 isomers Ex) C 20 H 42 366,319 isomers
Geometric Isomers Geometric isomers: have same covalent partnerships but differ in spatial arrangement These differences arise from inflexibility of double bonds SINGLE BONDS: allow atoms they join to rotate freely DOUBLE BONDS: don t permit such rotation
Geometric Isomers If a double bond joins 2 carbon atoms and each carbon also has 2 different atoms attached to it, then 2 distinct geometric isomers are possible: Ex) Consider a simple molecule with 2 double-bonded carbons, each of which has an H and X attached to it The arrangement of both X s on the same side of the double bond is called a CIS isomer The arrangement of the X s on opposite sides is called a TRANS isomer Even this subtle difference in shape between geometric isomers can dramatically effect biological activities of organic molecules Ex) Vision requires that a chemical compound in the eye called rhodopsin be changed from cis isomer to trans isomer (reaction is light-induced)
Enantiomers Enantiomers: isomers that are mirror images of each other You can think of them as left-handed and right-handed versions of a molecule Just as you right hand won t fit into a left-handed glove, the working molecules in a cell can distinguish the 2 versions by shape Usually one isomer is biologically active and the other is inactive In the ball-and-stick model shown in the figure (above), the middle carbon atom is called an asymmetric carbon because it is attached to 4 different atoms (or groups of atoms) The 4 groups can be arranged in space around the asymmetric carbon in 2 different ways that are mirror images
The concept of enantiomers is important in the pharmaceutical industry because 2 enantiomers of a drug may not be equally effective One of the isomers may even produce harmful effects (in some cases) Ex) Thalidomide drug prescribed for 1000s of pregnant women in late 1950s and early 1960s This drug was a mixture of 2 enantiomers One enantiomer reduced morning sickness (desired effect) The other enantiomer caused severe birth defects Furthermore, even if the good enantiomer is used in its purified form, some of it will soon convert to the bad enantiomer inside a patient s body The differing effects of enantiomers in the body demonstrate that organisms are sensitive to even the most subtle variations in molecular architecture This is another example of the emergent properties of molecules that depend on specific arrangement of their atoms Animation: L-Dopa
Ibuprofen and albuterol are also example of drugs whose enantiomers have different effects S and R are letters used in one system to distinguish enantiomers Ibuprofen: reduces inflammation and pain Commonly sold as a mixture of its 2 enantiomers S enantiomer is 100X more effective than R Albuterol: used to relax bronchial muscles, improving airflow in asthma patients Only R-albuterol is synthesized and sold as a drug S form actually counteracts the active R-form
Concept Check 4.2 1) Draw the structural formula for C 2 H 4. 2) Which molecules in Figure 4.5 (pp. 61) are isomers? For each pair, identify the type of isomer. 3) How are gasoline and fat chemically similar? 4) Can propane (C 3 H 8 ) form isomers?
Concept 4.3: A small number of chemical groups are key to the functioning of biological molecules
The distinctive properties of an organic molecule depend not only on arrangement of its carbon skeleton but also on molecular components (atoms) attached to skeleton Hydrocarbons can be thought of as the underlying framework for more complex organic molecules A number of chemical groups can replace one or more of the hydrogen atoms bonded to the carbon skeleton These groups may: Participate directly in chemical reactions or Contribute to function indirectly by their effects on molecular shape
The Chemical Groups Most Important in the Processes of Life Functional groups are the components of organic molecules that are most commonly involved in chemical reactions The number and arrangement of functional groups give each molecule its unique properties Ex) Consider the differences between male sex hormone testosterone and female sex hormone estradiol (a type of estrogen) Both are steroids with a common carbon skeleton in the form of 4 fused rings These sex hormones differ only in the chemical groups attached to their rings These subtle differences in molecular structure influence the development of anatomical and physiological differences between male and female vertebrates
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 The 1 st 6 groups can act as functional groups They are also hydrophilic and therefore increase the solubility of organic compounds in water The methyl group is not reactive Instead, it often acts as a recognizable tag on biological molecules
Hydroxyl Groups Hydroxyl group (-OH): a hydrogen atom bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule Not to be confused with a hydroxide ion (OH-) These are considered alcohols (their specific names usually end in ol) Ex) Ethanol the alcohol present in alcoholic beverages Functional Properties: Polar due to presence of electronegative oxygen atom Can form H-bonds with water molecules, helping dissolve the organic compounds to which it is attached (like sugars)
Carbonyl Groups Carbonyl group (-C=O): consists of a carbon atom joined to an oxygen atom by a double bond, including: Ketones: if carbonyl group is within a carbon skeleton (acetone) Aldehydes: if carbonyl group is at end of carbon skeleton (propanal) Functional Properties: Ketones and aldehydes may be structural isomers of one another with different properties (like acetone and propanal) Both groups are found in sugars, giving rise to 2 major groups of sugars: Aldoses: contain an aldehyde Ketoses: contain a ketone
Carboxyl Groups Carboxyl group (-COOH): when an oxygen atom is double-bonded to a carbon atom that is also bonded to a hydroxyl group (-OH) Compounds containing carboxyl groups are called carboxylic acids (or organic acids) Ex) acetic acid (gives vinegar its sour taste) Functional Properties: Has acidic properties (it s a source of H+ ions) because the covalent bond between oxygen and hydrogen is so polar Ex) Acetic acid dissociates into acetate ion Found in cells in ionized form (with 1 charge) These are called carboxylate ions
Amino Groups Amino group (-NH2): consists of a nitrogen atom bonded to 2 hydrogen atoms and to the carbon skeleton Compounds with amino groups are called amines Ex) Glycine because it also has a carboxyl group, glycine is both an amine and a carboxylic acid Compounds with both of these groups are called AMINO ACIDS Functional Properties: Acts as a base (can pick up an H+ from surrounding solution; water in living organisms) Ionizes (with +1 charge) under cellular conditions
Sulfhydryl Groups Sulfhydryl group (-SH): consists of a sulfur atom bonded to a hydrogen atom Resembles a hydroxyl group (-OH) in shape Compounds containing sulfhydryls are called THIOLS Ex) Cysteine an important sulfur-containing amino acid Functional Properties: 2 sulfhydryl groups can react, forming a covalent bond (this cross-linking helps stabilize protein structure) Cross-linking of cysteines in hair proteins maintains curliness or straightness of hair Straight hair can be curled with curlers by breaking and reforming the cross-linking bonds)
Phosphate Groups Phosphate group (-OPO3 2-): a phosphorus atom is bonded to 4 oxygen atoms and one of these oxygen atoms in bonded to carbon skeleton; 2 of the oxygens carry a negative charge Phosphate groups are ionized forms of phosphoric acid groups (-OPO3H2) Compounds containing phosphate groups are called organic phosphates Ex: glycerol phosphate takes part in many important chemical reactions in cells and provides backbone for phospholipids (most prevalent molecules in cell membrane) Functional Properties: Contributes negative charge to molecule of which it is a part (-2 when at end of molecule; -1 when located internally in chain of phosphates) Has potential to react with water, releasing energy (part of ATP)
Methyl Groups Methyl groups (-CH3): consists of a carbon atom bonded to 3 hydrogen atoms May be attached to a carbon or to a different atom Compounds containing methyl groups are called methylated compounds Ex) 5-Methyl cytidine component of DNA that has been modified by addition of methyl group Functional Properties: Addition of a methyl group to DNA or molecules bound to DNA affects expression of gene (how proteins are synthesized) Arrangement of methyl groups in male and female sex hormones affects their shape and function
ATP: An Important Source of Energy for Cellular Processes The phosphate molecule shown in the figure before shows a simple organic phosphate molecule A more complicated organic phosphate called adenosine triphosphate (ATP) has a very important function in the cell It is the primary energy-transferring molecule in the cell Consists of molecule of adenosine attached to a string of 3 phosphate groups
Where 3 phosphate groups are present in series, one phosphate may split off as a result of a reaction with water This reaction creates an inorganic phosphate ion (HOPO 2-3 ) This is abbreviated as a P with a circle around it and a subscript of I By losing a phosphate, ATP becomes adenosine diphosphate (ADP) This reaction releases energy that can be used by the cell
The Chemical Elements of Life: A Review Living matter consists mainly of carbon, oxygen, hydrogen, and nitrogen, with smaller amount of sulfur and phosphorus These elements all form strong covalent bonds, which is an essential characteristic in the structure of complex organic molecules Of all these elements, carbon is the most versatile, making possible a great diversity of organic molecules Each of these organic molecules have particular properties that emerge from their unique arrangement of the carbon skeleton and the chemical groups suspended to that skeleton, leading to the foundation of all biological diversity
Concept Check 4.3 1) What does the term amino acid signify about the structure of such a molecule? 2) What chemical change occurs when ATP reacts with water and releases energy? 3) Suppose you has an organic molecule such as glycine (see Figure 4.10, amino group example, pp. 65), and you chemically removed the NH 2 group and replaced it with COOH. Draw the structural formula for this molecule and speculate about its chemical properties.
You should now be able to: 1. Explain how carbon s electron configuration explains its ability to form large, complex, diverse organic molecules 2. Describe how carbon skeletons may vary and explain how this variation contributes to the diversity and complexity of organic molecules 3. Distinguish among the three types of isomers: structural, geometric, and enantiomer Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
4. 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 5. Explain how ATP functions as the primary energy transfer molecule in living cells Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings