Information

2.4: Carbon - Biology


Skills to Develop

  • Explain why carbon is important for life
  • Describe the role of functional groups in biological molecules

Cells are made of many complex molecules called macromolecules, such as proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids. The macromolecules are a subset of organic molecules (any carbon-containing liquid, solid, or gas) that are especially important for life. The fundamental component for all of these macromolecules is carbon. The carbon atom has unique properties that allow it to form covalent bonds to as many as four different atoms, making this versatile element ideal to serve as the basic structural component, or “backbone,” of the macromolecules.

Individual carbon atoms have an incomplete outermost electron shell. With an atomic number of 6 (six electrons and six protons), the first two electrons fill the inner shell, leaving four in the second shell. Therefore, carbon atoms can form up to four covalent bonds with other atoms to satisfy the octet rule. The methane molecule provides an example: it has the chemical formula CH4. Each of its four hydrogen atoms forms a single covalent bond with the carbon atom by sharing a pair of electrons. This results in a filled outermost shell.

Hydrocarbons

Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane (CH4) described above. We often use hydrocarbons in our daily lives as fuels—like the propane in a gas grill or the butane in a lighter. The many covalent bonds between the atoms in hydrocarbons store a great amount of energy, which is released when these molecules are burned (oxidized). Methane, an excellent fuel, is the simplest hydrocarbon molecule, with a central carbon atom bonded to four different hydrogen atoms, as illustrated in Figure (PageIndex{1}). The geometry of the methane molecule, where the atoms reside in three dimensions, is determined by the shape of its electron orbitals. The carbons and the four hydrogen atoms form a shape known as a tetrahedron, with four triangular faces; for this reason, methane is described as having tetrahedral geometry.

As the backbone of the large molecules of living things, hydrocarbons may exist as linear carbon chains, carbon rings, or combinations of both. Furthermore, individual carbon-to-carbon bonds may be single, double, or triple covalent bonds, and each type of bond affects the geometry of the molecule in a specific way. This three-dimensional shape or conformation of the large molecules of life (macromolecules) is critical to how they function.

Hydrocarbon Chains

Hydrocarbon chains are formed by successive bonds between carbon atoms and may be branched or unbranched. Furthermore, the overall geometry of the molecule is altered by the different geometries of single, double, and triple covalent bonds, illustrated in Figure (PageIndex{2}). The hydrocarbons ethane, ethene, and ethyne serve as examples of how different carbon-to-carbon bonds affect the geometry of the molecule. The names of all three molecules start with the prefix “eth-,” which is the prefix for two carbon hydrocarbons. The suffixes “-ane,” “-ene,” and “-yne” refer to the presence of single, double, or triple carbon-carbon bonds, respectively. Thus, propane, propene, and propyne follow the same pattern with three carbon molecules, butane, butane, and butyne for four carbon molecules, and so on. Double and triple bonds change the geometry of the molecule: single bonds allow rotation along the axis of the bond, whereas double bonds lead to a planar configuration and triple bonds to a linear one. These geometries have a significant impact on the shape a particular molecule can assume.

Hydrocarbon Rings

So far, the hydrocarbons we have discussed have been aliphatic hydrocarbons, which consist of linear chains of carbon atoms. Another type of hydrocarbon, aromatic hydrocarbons, consists of closed rings of carbon atoms. Ring structures are found in hydrocarbons, sometimes with the presence of double bonds, which can be seen by comparing the structure of cyclohexane to benzene in Figure (PageIndex{3}). Examples of biological molecules that incorporate the benzene ring include some amino acids and cholesterol and its derivatives, including the hormones estrogen and testosterone. The benzene ring is also found in the herbicide 2,4-D. Benzene is a natural component of crude oil and has been classified as a carcinogen. Some hydrocarbons have both aliphatic and aromatic portions; beta-carotene is an example of such a hydrocarbon.

Isomers

The three-dimensional placement of atoms and chemical bonds within organic molecules is central to understanding their chemistry. Molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds are known as isomers. Structural isomers (like butane and isobutene shown in Figure (PageIndex{4})a differ in the placement of their covalent bonds: both molecules have four carbons and ten hydrogens (C4H10), but the different arrangement of the atoms within the molecules leads to differences in their chemical properties. For example, due to their different chemical properties, butane is suited for use as a fuel for cigarette lighters and torches, whereas isobutene is suited for use as a refrigerant and a propellant in spray cans.

Geometric isomers, on the other hand, have similar placements of their covalent bonds but differ in how these bonds are made to the surrounding atoms, especially in carbon-to-carbon double bonds. In the simple molecule butene (C4H8), the two methyl groups (CH3) can be on either side of the double covalent bond central to the molecule, as illustrated in Figure (PageIndex{4})b. When the carbons are bound on the same side of the double bond, this is the cis configuration; if they are on opposite sides of the double bond, it is a trans configuration. In the trans configuration, the carbons form a more or less linear structure, whereas the carbons in the cis configuration make a bend (change in direction) of the carbon backbone.

Art Connection

Which of the following statements is false?

  1. Molecules with the formulas CH3CH2COOH and C3H6O2 could be structural isomers.
  2. Molecules must have a double bond to be cis-trans isomers.
  3. To be enantiomers, a molecule must have at least three different atoms or groups connected to a central carbon.
  4. To be enantiomers, a molecule must have at least four different atoms or groups connected to a central carbon.

In triglycerides (fats and oils), long carbon chains known as fatty acids may contain double bonds, which can be in either the cis or trans configuration, illustrated in Figure (PageIndex{5}). Fats with at least one double bond between carbon atoms are unsaturated fats. When some of these bonds are in the cis configuration, the resulting bend in the carbon backbone of the chain means that triglyceride molecules cannot pack tightly, so they remain liquid (oil) at room temperature. On the other hand, triglycerides with trans double bonds (popularly called trans fats), have relatively linear fatty acids that are able to pack tightly together at room temperature and form solid fats. In the human diet, trans fats are linked to an increased risk of cardiovascular disease, so many food manufacturers have reduced or eliminated their use in recent years. In contrast to unsaturated fats, triglycerides without double bonds between carbon atoms are called saturated fats, meaning that they contain all the hydrogen atoms available. Saturated fats are a solid at room temperature and usually of animal origin.

Enantiomers

Enantiomers are molecules that share the same chemical structure and chemical bonds but differ in the three-dimensional placement of atoms so that they are mirror images. As shown in Figure (PageIndex{6}), an amino acid alanine example, the two structures are non-superimposable. In nature, only the L-forms of amino acids are used to make proteins. Some D forms of amino acids are seen in the cell walls of bacteria, but never in their proteins. Similarly, the D-form of glucose is the main product of photosynthesis and the L-form of the molecule is rarely seen in nature.

Functional Groups

Functional groups are groups of atoms that occur within molecules and confer specific chemical properties to those molecules. They are found along the “carbon backbone” of macromolecules. This carbon backbone is formed by chains and/or rings of carbon atoms with the occasional substitution of an element such as nitrogen or oxygen. Molecules with other elements in their carbon backbone are substituted hydrocarbons.

The functional groups in a macromolecule are usually attached to the carbon backbone at one or several different places along its chain and/or ring structure. Each of the four types of macromolecules—proteins, lipids, carbohydrates, and nucleic acids—has its own characteristic set of functional groups that contributes greatly to its differing chemical properties and its function in living organisms.

A functional group can participate in specific chemical reactions. Some of the important functional groups in biological molecules are shown in Figure (PageIndex{7}); they include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl. These groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids. Functional groups are usually classified as hydrophobic or hydrophilic depending on their charge or polarity characteristics. An example of a hydrophobic group is the non-polar methane molecule. Among the hydrophilic functional groups is the carboxyl group found in amino acids, some amino acid side chains, and the fatty acids that form triglycerides and phospholipids. This carboxyl group ionizes to release hydrogen ions (H+) from the COOH group resulting in the negatively charged COO- group; this contributes to the hydrophilic nature of whatever molecule it is found on. Other functional groups, such as the carbonyl group, have a partially negatively charged oxygen atom that may form hydrogen bonds with water molecules, again making the molecule more hydrophilic.

Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the function of many macromolecules and help them to fold properly into and maintain the appropriate shape for functioning. Hydrogen bonds are also involved in various recognition processes, such as DNA complementary base pairing and the binding of an enzyme to its substrate, as illustrated in Figure (PageIndex{8}).

Summary

The unique properties of carbon make it a central part of biological molecules. Carbon binds to oxygen, hydrogen, and nitrogen covalently to form the many molecules important for cellular function. Carbon has four electrons in its outermost shell and can form four bonds. Carbon and hydrogen can form hydrocarbon chains or rings. Functional groups are groups of atoms that confer specific properties to hydrocarbon (or substituted hydrocarbon) chains or rings that define their overall chemical characteristics and function.

Art Connections

[link] Which of the following statements is false?

  1. Molecules with the formulas CH3CH2COOH and C3H6O2 could be structural isomers.
  2. Molecules must have a double bond to be cis-trans isomers.
  3. To be enantiomers, a molecule must have at least three different atoms or groups connected to a central carbon.
  4. To be enantiomers, a molecule must have at least four different atoms or groups connected to a central carbon.

[link] C

Review Questions

Each carbon molecule can bond with as many as________ other atom(s) or molecule(s).

  1. one
  2. two
  3. six
  4. four

D

Which of the following is not a functional group that can bond with carbon?

  1. sodium
  2. hydroxyl
  3. phosphate
  4. carbonyl

A

Free Response

What property of carbon makes it essential for organic life?

Carbon is unique and found in all living things because it can form up to four covalent bonds between atoms or molecules. These can be nonpolar or polar covalent bonds, and they allow for the formation of long chains of carbon molecules that combine to form proteins and DNA.

Compare and contrast saturated and unsaturated triglycerides.

Saturated triglycerides contain no double bonds between carbon atoms; they are usually solid at room temperature. Unsaturated triglycerides contain at least one double bond between carbon atoms and are usually liquid at room temperature.

Glossary

aliphatic hydrocarbon
hydrocarbon consisting of a linear chain of carbon atoms
aromatic hydrocarbon
hydrocarbon consisting of closed rings of carbon atoms
enantiomers
molecules that share overall structure and bonding patterns, but differ in how the atoms are three dimensionally placed such that they are mirror images of each other
functional group
group of atoms that provides or imparts a specific function to a carbon skeleton
geometric isomer
isomer with similar bonding patterns differing in the placement of atoms alongside a double covalent bond
hydrocarbon
molecule that consists only of carbon and hydrogen
isomers
molecules that differ from one another even though they share the same chemical formula
organic molecule
any molecule containing carbon (except carbon dioxide)
structural isomers
molecules that share a chemical formula but differ in the placement of their chemical bonds
substituted hydrocarbon
hydrocarbon chain or ring containing an atom of another element in place of one of the backbone carbons

Influence of multi-walled carbon nanotubes on the microbial biomass, enzyme activity, and bacterial community structure in 2,4-dichlorophenol-contaminated sediment

The rise in manufacture and use of carbon nanotubes has aroused the concern about their potential risks associated with coexisting pollutants in the aquatic environment. 2,4-dichlorophenol (2,4-DCP), with a high toxicity to many aquatic organisms, is a widespread pollutant resulting from the extensive use of pesticides and preservatives. In this article, the adsorption of 2,4-DCP by riverine sediment and the responses of sediment microbial community to 2,4-DCP were studied in the presence of multi-walled carbon nanotubes (MWCNTs). Adding MWCNTs significantly increased the adsorption amount of sediment for 2,4-DCP from 0.541 to 1.44 mg/g as the MWCNT concentration increased from 0 to 15 mg/g. The responses of sediment microbial community were determined after one-month exposure to MWCNTs at different concentrations (0.05, 0.5, 5, and 50 mg/g). The microbial biomass carbon in the sediment contaminated with 2,4-DCP increased in the presence of 5 mg/g of MWCNTs (from 0.06 to 0.11 mg/g), but not significantly changed at other MWCNT concentrations. For the sediments contaminated with 2,4-DCP, the presence of MWCNTs made no difference to urease activity, while the dehydrogenase activity slightly increased with the addition of 5 mg/g of MWCNTs and decreased in the presence of 50 mg/g of MWCNTs. The changes of sediment bacterial communities were further determined by 16S rRNA gene sequencing. Based on the weighted UniFrac distance between communities, the clustering analysis suggested that the contamination of 2,4-DCP affected the bacterial community structure in a greater degree than that caused by MWCNTs at relatively low concentrations (≤5 mg/g). Bacteroidetes, Planctomycetes, and Nitrospirae were feature bacterial phyla to reflect the effects of MWCNTs and 2,4-DCP on sediment bacterial community. These results may contribute to the understanding of microbial community response to co-exposure of MWCNTs and 2,4-DCP and the assessment of associated ecological risks.

Keywords: 16S rRNA gene 2,4-dichlorophenol Carbon nanotubes Microbial community Sediment.


4.2. Functional Groups

Functional groups are groups of atoms that occur within molecules and confer specific chemical properties to those molecules. They are found along the “carbon backbone” of macromolecules. This carbon backbone is formed by chains and/or rings of carbon atoms with the occasional substitution of an element such as nitrogen or oxygen. Molecules with other elements in their carbon backbone are substituted hydrocarbons.

The functional groups in a macromolecule are usually attached to the carbon backbone at one or several different places along its chain and/or ring structure. Each of the four types of macromolecules—proteins, lipids, carbohydrates, and nucleic acids—has its own characteristic set of functional groups that contributes greatly to its differing chemical properties and its function in living organisms. These macromolecules will be discussed further in Chapter 5.

A functional group can participate in specific chemical reactions. Some of the important functional groups in biological molecules are shown in Figure 4.8 they include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl. These groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids. Functional groups are usually classified as hydrophobic or hydrophilic depending on their charge or polarity characteristics. An example of a hydrophobic group is the non-polar methane molecule. Among the hydrophilic functional groups is the carboxyl group found in amino acids, some amino acid side chains, and the fatty acids that form triglycerides and phospholipids. This carboxyl group ionizes to release hydrogen ions (H + ) from the COOH group resulting in the negatively charged COO – group this contributes to the hydrophilic nature of whatever molecule it is found on. Other functional groups, such as the carbonyl group, have a partially negatively charged oxygen atom that may form hydrogen bonds with water molecules, again making the molecule more hydrophilic.

The Hydroxyl Group–Alcohols

The hydroxyl group takes its name from the hyd rogen and oxy gen atoms comprising this functional group. Molecules containing an hydroxyl group are called alcohols, and their names end in “alcohol” or “-OH”. Ethanol or ethyl alcohol, wit a molecule formula of CH3CH2OH, is a common alcohol that is found in wine, beer and spirits. Alcohols are polar molecules because of the oxygen, and the hydrogen attached to the oxygen readily forms hydrogen bonds with either oxygen or nitrogen of other atoms. Small alcohols, such as ethanol, readily form hydrogen bonds with water so are soluble in water. One or more hydroxyl groups may be attached to terminal or middle carbons. For example, glycerol which is found in lipids, has an hydroxyl group attached to each of its 3 carbons.

The Carbonyl Group–Aldehydes and Ketones

The carbonyl group is formed by removing the hydrogen from a hydroxyl and a hydrogen from the attached carbon to form a carbon-oxygen double bond. If this C=O is at the end of the molecule it is called an aldehyde if it is in the middle of the molecule, it is called a ketone. (A way to remember this is that the “a” of aldehyde is at the beginning of the alphabet and the “k” of ketone is in the middle of the alphabet.) Aldehydes are given the suffix of “-al” or “-aldehyde” ketones are given the suffix “-one”. If someone has been drinking alcohol, the liver will convert ethyl alcohol into the aldehyde acetaldehyde, sometimes called the hangover molecule. Because of its oxygen, aldehydes are polar, but without the hydrogen, they are unable to form hydrogen bonds with each other. Acetone, a major component in fingernail polish remover, evaporates much more quickly than water since it is not held in the liquid state by hydrogen bonds.

The Carboxyl Group–Carboxylic Acids

The Amino Group–The Amines

The Phosphate Group

The Sulfhydryl Group–The Thiols

The Methyl Group

The methyl group, which was recently added as a biological functional group, is a carbon to which 3 hydrogen atoms are attached, -CH3. Since it is a hydrocarbon, the methyl group is nonpolar. Methyl groups added to DNA or proteins associated with DNA will affect gene expression as we will see in Chapter 18.


2.4 Energy Enters Ecosystems Through Photosynthesis

All living organisms on Earth consist of one or more cells. Each cell runs on the chemical energy found mainly in carbohydrate molecules, and the majority of these molecules are produced by one process: photosynthesis. Through photosynthesis, certain organisms convert solar energy (sunlight) into chemical energy, which is then used to build carbohydrate molecules. The energy stored in the bonds to hold these molecules together is released when an organism breaks down food. Cells then use this energy to perform work, such as movement. The energy that is harnessed from photosynthesis enters the ecosystems of our planet continuously and is transferred from one organism to another. Therefore, directly or indirectly, the process of photosynthesis provides most of the energy required by living things on Earth. Photosynthesis also results in the release of oxygen into the atmosphere. In short, to eat and breathe humans depend almost entirely on the organisms that carry out photosynthesis.

Solar Dependence and Food Production

Some organisms can carry out photosynthesis, whereas others cannot. An autotroph is an organism that can produce its own food. The Greek roots of the word autotroph mean “self” (auto) “feeder” (troph). Plants are the best-known autotrophs, but others exist, including certain types of bacteria and algae (Figure 1 below). Oceanic algae contribute enormous quantities of food and oxygen to global food chains. More specifically, plants are photoautotrophs, a type of autotroph that uses sunlight and carbon from carbon dioxide to synthesize chemical energy in the form of carbohydrates. All organisms carrying out photosynthesis require sunlight.

Heterotrophs are organisms incapable of photosynthesis that must therefore obtain energy and carbon from food by consuming other organisms. The Greek roots of the word heterotroph mean “other” (hetero) “feeder” (troph), meaning that their food comes from other organisms. Even if the organism being consumed is another animal, it traces its stored energy back to autotrophs and the process of photosynthesis. Humans are heterotrophs, as are all animals and fungi. Heterotrophs depend on autotrophs, either directly or indirectly. For example, a deer obtains energy by eating plants. A wolf eating a deer obtains energy that originally came from the plants eaten by that deer (Figure 2 below). Using this reasoning, all food eaten by humans can be traced back to autotrophs that carry out photosynthesis.

Main Structures and Summary of Photosynthesis

Photosynthesis requires sunlight, carbon dioxide, and water as starting reactants (Figure 3 below). After the process is complete, photosynthesis releases oxygen and produces carbohydrate molecules, most commonly glucose. These sugar molecules contain the energy that living things need to survive. The complex reactions of photosynthesis can be summarized by the chemical equation shown in Figure 4 below.

Although the equation looks simple, the many steps that take place during photosynthesis are actually quite complex. In plants, photosynthesis takes place primarily in the chloroplasts of leaves. Chloroplasts have a double (inner and outer) membrane. Within the chloroplast is a third membrane that forms stacked, disc-shaped structures called thylakoids. Embedded in the thylakoid membrane are molecules of chlorophyll, a pigment (a molecule that absorbs light) through which the entire process of photosynthesis begins.

The Two Parts of Photosynthesis

Photosynthesis takes place in two stages: the light-dependent reactions and the Calvin cycle. In the light-dependent reactions chlorophyll absorbs energy from sunlight and then converts it into chemical energy with the aid of water. The light-dependent reactions release oxygen as a byproduct from the splitting of water. In the Calvin cycle, the chemical energy derived from the light-dependent reactions drives both the capture of carbon in carbon dioxide molecules and the subsequent assembly of sugar molecules.

The Global Significance of Photosynthesis

The process of photosynthesis is crucially important to the biosphere for the following reasons:


Watch the video: Carbon as a building block of life. Properties of carbon. Biology. Khan Academy (November 2021).