Ch. 4 Carbon & Molecular Diversity of Life Dynamic Study Module Flashcards

acid; amino

Ex.

Choose the pair of terms that completes this sentence about functional groups in organic chemistry: Carboxyl is to acid as amino is to base.

The carboxyl group is an acid and the amino group is a base. A carboxyl group has acidic properties because it can donate a proton (H⁺) to a solution because the covalent bond between oxygen and hydrogen is so polar.

The amino group acts as a base because it can pick up or accept a proton (H⁺) from a solution. In this way, they can be viewed as complementary because one, the acid, donates a proton and the other, the base, accepts a proton.

This same complementary pattern does not exist for the other answer choices.

6; 4; 4

Ex.

Carbon’s atomic number is 6. This means that it has 6 electrons. After completing the first energy level, carbon has 4 valence electrons and can form 4 bonds.

Carbon has 6 electrons, with 2 in the first electron shell and 4 in the second shell; thus, it has 4 valence electrons in a shell that can hold up to 8 electrons. A carbon atom usually completes its valence shell by sharing its 4 electrons with other atoms so that 8 electrons are present. Each pair of shared electrons constitutes a covalent bond. In organic molecules, carbon usually forms single or double covalent bonds. Each carbon atom acts as an intersection point from which a molecule can branch off in as many as four directions. This enables carbon to form large, complex molecules.

“4; 4; 4”; “6; 2; 2”; “12; 6; 6”; and “12; 4; 4” are incorrect because carbon has 6 electrons, with 2 in the first electron shell and 4 in the second shell; thus, it has 4 valence electrons in a shell that can hold up to 8 electrons.

R-COOH

Ex.

The R-COOH molecule is a weak acid.

The molecule with the carboxyl group (-COOH) is a weak acid because it can donate a proton (H⁺) as a result of the covalent bond between oxygen and hydrogen being so polar. The amino (-NH₂), sulfhydryl (-SH), and hydroxyl (-OH) groups cannot donate protons (H⁺).

water (H₂O)

Ex.

Biologically important chemical groups include all of the following except water (H₂O).

The seven chemical groups most important in biological processes are the hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl groups. The first six groups can be chemically reactive; of these, all except the sulfhydryl group are also hydrophilic and thus increase the solubility of organic compounds in water. The methyl group is not reactive but instead often serves as a recognizable tag on biological molecules. Study the figure below to become familiar with these biologically important chemical groups.

“Carboxyl group (-COOH),” “amine group (-NH₂),” “sulfhydryl group (-SH),” and “phosphate group (-PO₃ ^–2)” are four of the seven chemical groups most important in biological processes. Since this is an except question, all of these answers are incorrect.

Sulfhydryl

Ex.

The sulfhydryl is the functional group not present in this molecule.

The sulfhydryl group (-SH) consists of a sulfur atom bonded to an atom of hydrogen and resembles a hydroxyl group in shape.

Carboxyl, hydroxyl, and amino groups are all present in the depicted molecule.

called hydrocarbons

Ex.

Molecules that contain only carbon and hydrogen are called hydrocarbons.

All of the molecules that are shown in the two figures below are hydrocarbons, organic molecules consisting of only carbon and hydrogen. Atoms of hydrogen are attached to the carbon skeleton wherever electrons are available for covalent bonding. Hydrocarbons are the major components of petroleum, which is called a fossil fuel because it consists of the partially decomposed remains of organisms that lived millions of years ago. Although hydrocarbons are not prevalent in most living organisms, many of a cell’s organic molecules have regions consisting of only carbon and hydrogen.

“Called hydrated carbons” is incorrect because the molecules contain hydrogen, carbon, and oxygen.

“Called inorganic carbons” is incorrect because any molecule that contains carbon and hydrogen is organic.

“Found only as linear chains” is incorrect because the molecules can be branched, have double bonds, and form rings.

may not be equally effective

Ex.

In the pharmaceutical industry, two enantiomers of a drug may not be equally effective.

The concept of enantiomers is important in the pharmaceutical industry because the two enantiomers of a drug may not be equally effective, as is the case for both ibuprofen and the asthma medication albuterol. Methamphetamine also occurs in two enantiomers that have very different effects. One enantiomer is the highly addictive stimulant drug known as “crank,” sold illegally in the street drug trade. The other has a much weaker effect and is the active ingredient in an over-the-counter vapor inhaler for the treatment of nasal congestion. The differing effects of enantiomers in the body demonstrate that organisms are sensitive to even the most subtle variations in molecular architecture. Once again, we see that molecules have emergent properties that depend on the specific arrangement of their atoms.

“Are always produced as a mixture” is incorrect because in some cases, an enantiomer may be highly addictive or it may counteract the active form, as in albuterol.

“Are equally effective” is incorrect because usually, only one isomer is biologically active because only that form can bind to specific molecules in an organism.

“Never counteract each other” is incorrect because as in the case of albuterol, only the R form is synthesized and sold because the S form counteracts the active R form.

“Are equally safe in either form” is incorrect because some enantiomers can be highly addictive drugs.

methyl group (-CH₃)

Ex.

The chemical group that is involved in regulating DNA is the methyl group (^-CH₃) because it affects the expression of genes when on DNA or on proteins bound to DNA.

“Amine group (^-NH₂)” is incorrect because this group acts as a base and can remove an H⁺ from the surrounding solution.

“Sulfhydryl group (^-SH)” is incorrect because two -SH groups can react, forming a “cross-link” that helps stabilize protein structure.

“Phosphate group (-PO₃ ^–2)” is incorrect because it contributes negative charge (1– when positioned inside a chain of phosphates; 2– when at the end). When attached, it confers on a molecule the ability to react with water, releasing energy.

“Carboxyl group (^-COOH)” is incorrect because it acts as an acid (can donate H⁺) because the covalent bond between oxygen and hydrogen is so polar.

abiotic compounds cycled through the apparatus and were sampled for organic compounds

Ex.

In Miller’s 1953 laboratory experiment, abiotic compounds cycled through the apparatus and were sampled for organic compounds.

In 1953, Stanley Miller, a graduate student of Harold Urey’s at the University of Chicago, helped bring the abiotic (nonliving) synthesis of organic compounds into the context of evolution. From his results, Miller concluded that complex organic molecules could arise spontaneously under conditions thought at that time to have existed on the early Earth. These experiments supported the idea that abiotic synthesis of organic compounds, perhaps near volcanoes, could have been an early stage in the origin of life.

“Organic compounds were added to the seawater and decomposed” is incorrect because abiotic molecules were added to the seawater in the initial step.

“Condensed molecules never contained organic compounds” is incorrect because the condensed “cooled rain” contained organic molecules.

“The experiment was not useful in supporting evolution” is incorrect because although the jury is still out, these experiments do support the idea of abiotic synthesis of organic compounds.

“The atmosphere in the experiment contained O₂” is incorrect because the atmosphere contained a mixture of ammonia, methane, and hydrogen gas.

One enantiomer may provide an effective treatment whereas the other may be ineffective or even toxic.

Ex.

One enantiomer may provide an effective treatment whereas the other may be ineffective or even toxic.

It is important for pharmaceutical companies to sell only single-enantiomer drugs because two enantiomers of a drug may not be equally effective. For example, both ibuprofen and the asthma medication albuterol have different pharmaceutical behaviors. In addition, methamphetamine also occurs in two enantiomers that have very different effects. One enantiomer is the highly addictive stimulant drug known as “crank,” sold illegally in the street drug trade. The other has a much weaker effect and is even found as an ingredient in an over-the-counter vapor inhaler for treatment of nasal congestion. It is expensive to manufacture these single-enantiomer drugs but it is important because only one or the other of the isomers, although occasionally both, will be safe. It is also important to understand if the enantiomers spontaneously flit between forms, which can but doesn’t always happen in the body.

a variety of simple organic compounds could be spontaneously synthesized from components in Earth's primitive atmosphere

Ex.

Stanley Miller's experiments were significant because he demonstrated that a variety of simple organic compounds could be spontaneously synthesized from components in Earth's primitive atmosphere.

Stanley Miller's experiments were significant because he showed that complex organic molecules, not volcanic outgassings, could arise spontaneously under conditions thought to have existed on the early Earth. His work helped bring the abiotic (nonliving) synthesis of organic compounds into the context of evolution and to shift the mainstream of biological thought from vitalism to mechanism, the view that physical and chemical laws govern all natural phenomena. Earlier work by Friedrich Wöhler showed that urea could be synthesized in the lab.

lacking hydrogen atoms

Ex.

The carbon skeleton can vary in all of the following except lacking hydrogen atoms.

Carbon chains form the skeletons of most organic molecules. The skeletons vary in length and may be straight, branched, or arranged in closed rings. Some carbon skeletons have double bonds, which vary in number and location. Such variation in carbon skeletons is one important source of the molecular complexity and diversity that characterize living matter. In addition, atoms of other elements can be bonded to the skeletons at available sites.

“Length,” “branching,” “double bond position,” and “presence of rings” are all characteristics of the carbon skeleton and therefore are incorrect answers because this is an except question.

Both -COOH and -NH₂

_Ex.

Both -COOH and -NH₂ are found in all amino acids.

All amino acids contain at least one carboxyl functional group and one amino functional group. In addition, it may contain one or more of the other functional groups.

mirror-image isomers of a molecule

Ex.

Enantiomers are mirror-image isomers of a molecule.

Enantiomers are isomers that are mirror images of each other and that differ in shape due to the presence of an asymmetric carbon, one that is attached to four different atoms or groups of atoms. The four groups can be arranged in space around the asymmetric carbon in two different ways that are mirror images. Enantiomers are, in a way, left-handed and right-handed versions of the molecule. Just as your right hand won’t fit into a left-handed glove, a “right-handed” molecule won’t fit into the same space as the “left-handed” version. Usually, only one isomer is biologically active because only that isomer can bind to specific molecules in an organism.

“Structural isomers of a molecule” is incorrect because structural isomers have different covalent arrangement of their atoms.

“Cis-trans isomers of a molecule” is incorrect because in this case, the carbons have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to the inflexibility of double bonds.

“Molecules that can be tightly packed because they are unsaturated” is incorrect because unsaturated molecules cannot be tightly packed and also exist as liquids.

“Not important in drug development” is incorrect because the two enantiomers of a drug may not be equally effective.

ATP stores the potential to react with water, thereby removing a phosphate group and releasing energy for cellular processes.

Ex.

ATP stores the potential to react with water, thereby removing a phosphate group and releasing energy for cellular processes.

ATP (adenosine triphosphate) is important to the cell because it can react with water, forming inorganic phosphate and ADP (adenosine diphosphate). This reaction releases energy that can be used by the cell. ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups. Where three phosphates are present in series, as in ATP, one phosphate may be split off as a result of a reaction with water.

Although ATP is sometimes said to store energy, it is more accurate to think of it as storing the potential to react with water.

ATP does not have a long hydrocarbon tail. It is a relatively small molecule that easily moves through the cell and across the cell membrane, but it is not a component of cell membranes.

Carbon, nitrogen, oxygen, hydrogen, phosphate, and sulfur

Ex.

The six most important chemical elements of life are carbon, nitrogen, oxygen, hydrogen, phosphate, and sulfur.

Of these chemical elements, carbon is unparalleled in its ability to form molecules that are large, complex, and varied, making possible the diversity of organisms that have evolved on Earth. Proteins, DNA, carbohydrates, and other molecules that distinguish living matter from inanimate material are all composed of carbon atoms bonded to one another and to atoms of these other elements. These elements all form strong covalent bonds, an essential characteristic in the architecture of complex organic molecules. Elements such as iron (Fe), calcium (Ca), magnesium (Mg), and zinc (Zn), although important to life, are readily available in the environment and serve specialized rather than central roles in the formation of complex, life-dependent molecules.

Amino

Ex.

The chemical group that is most likely to be responsible for an organic molecule behaving as a base is the amino group (-NH₂) because it acts as a base and can pick up a proton (H⁺) from the surrounding solution (water, in living organisms). It consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton.

Hydroxyl, carboxyl, carbonyl, and phosphate groups do not accept protons.

Carbon

Ex.

The element that is always associated with organic chemistry is carbon.

Most, but not all, organic compounds also contain hydrogen atoms in addition to carbon.

Sulfur, nitrogen, hydrogen, and oxygen are also common in organic compounds, but they are not always present.

carboxyl group (-COOH)

Ex.

The chemical group that acts as an acid is the carboxyl group (-COOH). It acts as an acid (can donate H⁺) because the covalent bond between oxygen and hydrogen is so polar.

“Amine group (-NH₂)” is incorrect because this group acts as a base and can remove an H⁺ from the surrounding solution.

“Sulfhydryl group (-SH)” is incorrect because two -SH groups can react, forming a “cross-link” that helps stabilize protein structure.

“Phosphate group (-PO₃ ^–2)” is incorrect because it contributes a negative charge (1- when positioned inside a chain of phosphates; 2- when at the end). When attached, it confers on a molecule the ability to react with water, releasing energy.

“Methyl group (-CH₃)” is incorrect because it affects the expression of genes when on DNA or on proteins bound to DNA. It also affects the shape and function of male and female sex hormones.

cis-trans isomers

Ex.

When a double bond joins two carbon atoms, cis-trans isomers can form. In cis-trans isomers (formerly called geometric isomers), carbons have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to the inflexibility of double bonds. Single bonds allow the atoms they join to rotate freely about the bond axis without changing the compound. In contrast, double bonds do not permit such rotation. If a double bond joins two carbon atoms and each C also has two different atoms (or groups of atoms) attached to it, then two distinct cis-trans isomers are possible. Consider a simple molecule with two double-bonded carbons, each of which has an H and an X attached to it. The arrangement with both Xs on the same side of the double bond is called a cis isomer, and that with the Xs on opposite sides is called a trans isomer. The subtle difference in shape between such isomers can dramatically affect the biological activities of organic molecules. For example, the biochemistry of vision involves a light-induced change of retinal, a chemical compound in the eye, from the cis isomer to the trans isomer.

“Structural isomers” is incorrect because these isomers have different covalent arrangements of their atoms.

“Enantiomers” is incorrect because these are mirror images of a molecule.

“Saturated fats” is incorrect because saturated hydrocarbons do not have double bonds.

“Chemical groups” is incorrect because they contribute to the molecular shape of a molecule and its unique properties.

R-NH₂

Ex.

The molecule R-NH₂ is a weak base.

The molecule with the amino group (-NH₂) is a weak base because it can accept a proton (H⁺) from the surrounding solution (water in living organisms), which is the behavior of a base. The hydroxyl group (-OH) cannot accept a proton, and the carboxyl group (-COOH) can donate but not accept a proton.

Hydrophobic, nonpolar, and a good source of stored energy

Ex.

Hydrocarbons are organic molecules consisting of only carbon and hydrogen. Their properties include being hydrophobic, nonpolar, and a good source of stored energy.

They are not charged and do not contain functional groups, such as carboxyl and amine groups, like many other organic compounds. Hydrocarbons are hydrophobic because the great majority of their bonds are relatively nonpolar carbon-to-hydrogen linkages. They can undergo reactions that release a relatively large amount of energy. The gasoline that fuels a car consists of hydrocarbons, and the hydrocarbon tails of fats serve as stored fuel for animals. They are the major components of petroleum, which is called a fossil fuel because it consists of the partially decomposed remains of organisms that lived millions of years ago.

ATP

Ex.

When three phosphate groups are covalently attached to adenosine, ATP is formed.

The “Phosphate group” row in the chemical groups figure below shows a simple example of an organic phosphate molecule. A more complicated organic phosphate, adenosine triphosphate, or ATP, is worth mentioning here because its function in a cell is so important. ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups: Where three phosphates are present in a series, as in ATP, one phosphate may be split off as a result of a reaction with water. This inorganic phosphate ion, HOPO₃ ^2–, is often abbreviated Pi in this book, and a phosphate group in an inorganic molecule is often written as P_i. Having lost one phosphate, ATP becomes adenosine diphosphate, or ADP. Although ATP is sometimes said to store energy, it is more accurate to think of it as storing the potential to react with water. This reaction releases energy that can be used by a cell.

“ADP” is incorrect because it has only two phosphate groups and is adenosine diphosphate.

“AMP” is incorrect because it has only one phosphate group and is adenosine monophosphate.

“P_i” is incorrect because it is an inorganic phosphate.

“Glycerol phosphate” is incorrect because it is not adenosine triphosphate (ATP).

organic carbon always has a hydrogen atom covalently attached to it

Ex.

Inorganic carbon such as CO₂ differs from organic carbon because organic carbon always has a hydrogen atom covalently attached to it.

In the carbon dioxide molecule (CO₂), a single carbon atom is joined to two atoms of oxygen by double covalent bonds. The structural formula for CO₂ is shown here: O=C=O. Each line in a structural formula represents a pair of shared electrons. Thus, the two double bonds in CO₂ have the same number of shared electrons as four single bonds. The arrangement completes the valence shells of all atoms in the molecule. Because CO₂ is a very simple molecule and lacks hydrogen, it is often considered inorganic even though it contains carbon. Whether we call CO₂ organic or inorganic, however, it is clearly important to the living world as the source of carbon for all organic molecules in organisms.

“Inorganic carbon always has double bonds and organic carbon never has double bonds” is incorrect because both inorganic and organic carbon can form double bonds.

“Inorganic carbon always has a hydrogen atom covalently attached to it” is incorrect because inorganic carbon lacks hydrogen atoms.

“CO₂ is an example of an organic molecule” is incorrect because carbon dioxide lacks hydrogen atoms and is classified as an inorganic form of carbon.

they contribute to the molecular shape of a molecule and its unique properties

Ex.

Chemical groups are significant because they contribute to the molecular shape of a molecule and its unique properties.

The properties of an organic molecule depend not only on the arrangement of its carbon skeleton but also on the chemical groups attached to that skeleton. We can think of hydrocarbons, the simplest organic molecules, as the underlying framework for more complex organic molecules. A number of chemical groups can replace one or more hydrogen molecules of the hydrocarbon. These groups may participate in chemical reactions or may indirectly contribute to function by their effects on molecular shape; they help give each molecule its unique properties. Consider the differences between estradiol (a type of estrogen) and testosterone. These compounds are female and male sex hormones, respectively, in humans and other vertebrates. Both are steroids, organic molecules with a common carbon skeleton in the form of four fused rings. They differ only in the chemical groups attached to the rings (shown here in abbreviated form); the distinctions in molecular architecture are shaded in blue:

The different actions of these two molecules on many targets throughout the body are the basis of gender, producing the contrasting features of male and female vertebrates. In this case, the chemical groups are important because they affect molecular shape, thus contributing to function.

“They are always the same and do not influence the properties of a molecule” is incorrect because each chemical group contributes to the unique properties of a molecule.

“They can never be substituted” is incorrect because substitution of chemical groups contributes to the unique properties of a molecule.

“They stabilize a molecule by preventing chemical reactions” is incorrect because when chemical groups are involved in chemical reactions, they are called functional groups.

all help give each biological molecule its unique properties

Ex.

Although the structures of the functional groups that are most important to life vary, they share one thing in common: They all help give each biological molecule its unique properties.

The seven chemical groups most important in biological processes are the hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl groups. The first six groups can be chemically reactive; of these six, all except the sulfhydryl group are also hydrophilic and thus increase the solubility of organic compounds in water. The methyl group is not reactive, but instead often serves as a recognizable tag on biological molecules.

They do not all contain oxygen and they do not all have double bonds.

In addition, their reactive nature does not force straight-chain hydrocarbons into rings or cause a bonded carbon to be asymmetric, which is a property of the molecule and not the attached functional group.

a carbon atom can complete its valence shell by forming four covalent bonds

Ex.

The carbon atom is tetravalent; this means that a carbon atom can complete its valence shell by forming four covalent bonds.

Carbon possesses a total of six electrons, two in its inner shell and four in its valence (outer) shell and is called tetravalent, which means that it can form four covalent bonds with other atoms or groups of atoms to complete its outer shell of eight. Carbon, with a valence of four, can bond to various other atoms but especially to other carbon atoms, forming the carbon skeletons of organic compounds.

It forms a tetrahedron shape when it bonds with four other atoms.

Carbon is unlikely to form ionic bonds, which would require it to lose or gain an electron.

One enantiomer may provide an effective treatment whereas the other may be ineffective or even toxic.

Ex.

One enantiomer may provide an effective treatment whereas the other may be ineffective or even toxic.

It is important for pharmaceutical companies to sell only single-enantiomer drugs because two enantiomers of a drug may not be equally effective. For example, both ibuprofen and the asthma medication albuterol have different pharmaceutical behaviors. In addition, methamphetamine also occurs in two enantiomers that have very different effects. One enantiomer is the highly addictive stimulant drug known as “crank,” sold illegally in the street drug trade. The other has a much weaker effect and is even found as an ingredient in an over-the-counter vapor inhaler for treatment of nasal congestion. It is expensive to manufacture these single-enantiomer drugs but it is important because only one or the other of the isomers, although occasionally both, will be safe. It is also important to understand if the enantiomers spontaneously flit between forms, which can but doesn’t always happen in the body.

sulfhydryl group (-SH)

Ex.

The chemical group that helps stabilize protein structure is the sulfhydryl group (-SH).

Two -SH groups can react, forming a “cross-link” that helps stabilize protein structure. Hair protein cross-links maintain the straightness or curliness of hair; in hair salons, permanent treatments break cross-links and then re-form them while the hair is in the desired shape.

“Carboxyl group (-COOH)” is incorrect because the group acts as an acid and can donate an H⁺ to the surrounding solution.

“Amine group (-NH₂)” is incorrect because this group acts as a base and can remove an H⁺ from the surrounding solution.

“Phosphate group (-PO₃ ^–2)” is incorrect because it contributes negative charge (1– when positioned inside a chain of phosphates; 2– when at the end). When attached, this group confers on a molecule the ability to react with water, releasing energy.

“Methyl group (-CH₃)” is incorrect because it affects the expression of genes when on DNA or on proteins bound to DNA. It also affects the shape and function of male and female sex hormones.

Structural isomers

Ex.

The term that correctly describes the relationship between these two sugar molecules is structural isomer because they differ in the covalent arrangements of their atoms. Structural isomers may also differ in the location of double bonds.

In contrast, cis-trans isomers (formerly called geometric isomers), have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to the inflexibility of double bonds.

Enantiomers are isomers that are mirror images of each other and that differ in shape due to the presence of an asymmetric carbon, one that is attached to four different atoms or groups of atoms.

Finally, the same element may for different isotopes when it has the same number of protons but different numbers of neutrons.

the same molecular formula but different covalent arrangements of their carbon skeletons

Ex.

Structural isomers have the same molecular formula but different covalent arrangements of their carbon skeletons.

Structural isomers differ in the covalent arrangements of their atoms. Compare, for example, the two five-carbon compounds in shown in part a of the figure below. Both have the molecular formula C₅H₁₂, but they differ in the covalent arrangement of their carbon skeletons. The skeleton is straight in one compound but branched in the other. The number of possible isomers increases tremendously as carbon skeletons increase in size. There are only three forms of C₅H₁₂, but there are 18 variations of C₈H₁₈ and 366,319 possible structural isomers of C₂₀H₄₂. Structural isomers may also differ in the location of double bonds.

“A different molecular formula and the same covalent arrangement of their carbon skeletons” and “the same molecular formula and the same covalent arrangement of their carbon skeletons” are incorrect because structural isomers have the same molecular formula but differ in the covalent arrangements of their carbon skeletons.

“Different functional groups” is incorrect because the groups would result in different chemical formulas.

“Left- and right-handed forms” is incorrect because this describes an enantiomer.