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Biology 230 - Molecules and Cells

Properties of Macromolecules II-Nucleic Acids, Polysaccharides and Lipids

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Terms

  • alpha glycosidic bond
  • adenine (A)
  • amphipathic
  • beta glycosidic bond
  • base pair (bp)
  • carbohydrate
  • cellulose
  • cholesterol
  • complementary
  • cytosine (C)
  • deoxyribonucleic acid (DNA)
  • deoxyribose
  • disaccharide
  • D-glucose
  • DNA duplex
  • double-stranded
  • fatty acid
  • glycerol
  • glycogen
  • glycosidic bond
  • guanine (G)
  • hydrocarbon
  • lipid
  • messenger RNA (mRNA)
  • monosaccharide
  • nitrogenous base
  • nucleotide
     
  • partially hydrogenated fat
  • phosphodiester bond
  • phospholipid
  • polysaccharide
  • polyunsaturated fatty acid
  • purine
  • pyrimidine
  • replication
  • ribonucleic acid (RNA)
  • ribose
  • ribosomal RNA (rRNA)
  • ribosome
  • saturated fatty acid
  • single-stranded
  • starch
  • sterol
  • sugar-phosphate backbone
  • terpene
  • thymidine (T)
  • transcription
  • transfer RNA (tRNA)
  • translation
  • triacylglycerol
  • unsaturated fatty acid
  • uracil (U)

Introduction and Goals

There are four major families of macromolecules (proteins, nucleic acids, polysaccharides and lipids) that make up the bulk of the carbon content in a typical cell. In the previous tutorial we reviewed the structure and properties of proteins. In this tutorial we will examine the structures and properties of nucleic acids, polysaccharides and lipids. We will explore the distinct characteristics these macromolecules possess and review the roles they play in a typical cell. By the end of this tutorial you should know:

  • The basic structure of a nucleotide
  • The difference between DNA and RNA
  • How nucleotides are linked to form a single strand of nucleic acid chain
  • How two chains are held together in a double-stranded nucleic acid
  • How six-carbon sugars are linked together to form a disaccharide and a polysaccharide
  • The difference between alpha and beta glycosidic bonds
  • The general properties of lipids
  • The properties of saturated fatty acids and unsaturated fatty acids
  • The basic structure of several lipids, including triacylglycerols, phospholipids, sterols and terpenes

Nucleic Acids

Nucleic acids encode the genetic information of a cell

 Nucleic acids are macromolecules that store, transmit and express the genetic information of a cell. There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). In most cells, DNA is the stored form of genetic information transmitted from one generation to the next. DNA is copied in a process called replication and transmitted to the daughter cells. Genes are composed of DNA, and in eukaryotic cells most of the DNA is assembled into chromosomes in the nucleus. DNA is copied into RNA, which, in turn, directs protein synthesis. There are three major types of RNA. Messenger RNA (mRNA), a relatively short-lived intermediate copy of the DNA sequence, is synthesized in a process termed transcription. The mRNA directs protein synthesis, which is mediated by the ribosomes. A ribosome is a complex of proteins and RNA that guides the efficient and correct translation of the mRNA sequence into a protein sequence. The flow of information is from DNA to mRNA to protein. Ribosomal RNA (rRNA) is a structural RNA component of the ribosome. *Transfer RNA (tRNA)*delivers the amino acid to be incorporated into the growing peptide chain to the ribosome. The precise molecular mechanisms of transcription and translation will be discussed in future tutorials.

A nucleic acid is a polymer of nucleotides

Figure 1. Components of a nucleic acid.The general structure of a single-stranded nucleic acid chain and a nucleotide are illustrated. The three components of a nucleotide (the nitrogenous bases, the sugars and the phosphate group) are shown in the blue frames. Purines are shaded green and pyrimidines are shaded yellow. The sugars and phosphate group are shaded red. Note that the carbons in both the ribose and deoxyribose have been numbered and that the differences between these two sugars are boxed.

Both DNA and RNA are long polymers of nucleotides. A nucleotide has three distinct components: a 5-carbon sugar, a nitrogenous base, and a phosphate (PO4) group. The base is linked to the first-position carbon of the sugar, and the phosphate is linked to the fifth-position carbon (see Figure 1). There are two classes of nitrogenous bases: pyrimidines, which are single-ringed compounds; and purines, which are double-ringed compounds. DNA contains the purines adenine (A) and guanine (G), and the pyrimidines cytosine (C) and thymidine (T). RNA contains the same bases, with the exception of thymidine, which is replaced by uracil(U). Nucleotides are distinguished by their bases, and are also referred to by their bases. For instance, adenosine monophosphate is the nucleotide in RNA that contains the base adenine, but it is generally referred to as adenine. 

There are several differences between the nucleotides that make up DNA and RNA, including their five-carbon sugar. In RNA the sugar is ribose, and in DNA it is deoxyribose; hence, the origin of the names ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). These sugars differ in their second-position carbon, which is linked to a hydroxyl group (OH) in RNA and a hydrogen (H) in DNA. Three nucleotides in DNA have bases identical to nucleotides in RNA - they are, adenine, guanine and cytosine. In DNA, the fourth base is thymidine (T); in RNA, it is uracil (U). The phosphate groups are identical for DNA and RNA.

Nucleotides are Linked Via Phosphodiester Bonds

animation
(phosphodiester bond formation)

A nucleic acid chain is formed by covalent bonds between nucleotides. The linkage is termed a phosphodiester bondand it occurs between the sugar portion of the first nucleotide and the phosphate group of the second nucleotide (see animation). The phosphodiester bonds in RNA and DNA are identical because they involve functional groups identical for all nucleotides. There is an inherent directionality to the growth of a nucleic acid. Each new nucleotide is added to a hydroxyl (OH) group at position 3 in the sugar of the previous nucleotide via its phosphate group. Therefore, the first nucleotide has a free phosphate group linked to the fifth-position carbon in the sugar, and the last nucleotide has a free hydroxyl group at the third-position carbon of the sugar. This defines the directionality of the nucleic acid chain as 5' to 3', going from the first to the last nucleotide. The nucleotide sequence is abbreviated to the single letter designation for the base of each nucleotide (A, C, G and T or U). It is conventional to always write the sequence in the 5' to 3' direction.


DNA is a Double-Stranded Helix

Figure 2. The DNA duplex.The sugar-phosphate backbone is illustrated in red as the sides of the ladder. The base pairs are represented as rungs of the ladder. Adenine is complementary to thymine, and guanine is complementary to cytosine. The two strands of the DNA duplex are antiparallel. Most double-stranded DNA is found in a right-handed helix (shown on the right). One full turn of a typical DNA helix is 3.4 nm, encompassing approximately 10 base pairs per turn. The width of the helix is approximately 2 nm.

Figure 3. Hydrogen bonding of base pairs in double-stranded DNA.The hydrogen bonds in this illustration are represented by dashed lines. Note that the adenine-thymine base pair has only two hydrogen bonds, whereas the guanine-cytosine base pair has three hydrogen bonds. The sugar-phosphate backbone is illustrated in red.

DNA is often double-stranded, with the two strands of the nucleic acid held together by hydrogen bonding. However, it should be noted that in some instances RNA can be double-stranded and DNA can be single-stranded. In this tutorial, we will discuss double-stranded DNA. The two strands of DNA are held together by hydrogen bonds that form between the nitrogenous bases of two nucleotides on opposite strands. Figure 2 illustrates a DNA duplex. Imagine that the two stands of DNA, termed a DNA duplex, is a ladder. Each side of the ladder represents the sugar-phosphate backboneof the individual strands. The rungs of the ladder represent the nitrogenous bases of a pair of nucleotides from opposite stands held together by hydrogen bonds. The term base pair (bp) describes a pair of nucleotides held together by hydrogen bonds in the DNA duplex. There are strict rules that govern which nucleotides can form a base pair; adenine pairs with thymine, and cytosine pairs with guanine. The nucleotides that form a base pair are referred to as complementary; therefore, adenine is complementary to thymine, and guanine is complementary to cytosine. Base pairs differ in their number of hydrogen bonds. A C-G base pair is held together by three hydrogen bonds, whereas an A-T (or A-U) base pair is held together by only two hydrogen bonds. This is illustrated in Figure 3.

The DNA double helix consists of two complementary strands of DNA that run in opposite directions around the axis of the helix. The complementary strands are antiparallel (recall parallel and antiparallel orientations of beta sheets in Tutorial entitled Properties of Macromolecules I- Proteins). Moving down the helix, one strand runs 5' to 3' and the complementary strand runs 3' to 5'. The DNA duplex is not flat, but instead it is twisted such that the two strands of DNA are wound around each other in a double helix. The sugar phosphate backbone is on the outside surface of the double helix and the bases are buried in the center of the helix. Most double-stranded DNA is present in a right-handed double helix (see Figure 2).



Polysaccharides

Polysaccharides are storage and structural macromolecules

Polysaccharides function as stored forms of carbohydrates (macromolecules composed of carbon, hydrogen and oxygen in an approximate ratio of 1:2:1). Glycogen is the most common polysaccharide in animal cells, and starch and celluloseare the most common in plant cells. Cellulose also functions as a structural molecule in plants and it is a major component of the plant cell wall.

Polysaccharides are polymers of glucose

Figure 4. Alpha and beta configurations of D-glucose. alpha-D-glucose is shown in blue and beta-D-glucose is shown in green. The carbons are numbered. Note the hydroxyl groups at the first-position carbons.

Polysaccharides are long chains of repeating simple sugars. The most common polysaccharides (starch, glycogen and cellulose) are polymers of the same monosaccharide, D-glucose. D-glucose is a ringed, six-carbon sugar that exists in two configurations: alpha and beta (see Figure 4). These two forms are structurally identical, except for the position of the hydroxyl group on the first-position carbon. The hydroxyl group points down in alpha-D-glucose and it points up in beta-D-glucose. This seems like a trivial difference, but, as you will soon learn, this can have a significant impact.

Glycosidic Bonds

Glucose and other sugars are linked together via glycosidic bonds

Figure 5. Common disaccharides. Maltose and lactose are shown. alpha-D-glucose is shown in blue and beta-D-glucose and beta-D-galactose are shown in green. The alpha glycosidic bond in maltose and beta glycosidic bond in lactose are indicated.

In humans, glucose circulates in the blood as a simple monosaccharide. However, in many other organisms it circulates as a disaccharide (two monosaccharides linked via a covalent bond). The bond that links two monosaccharides is termed a glycosidic bond. It is formed by a condensation reaction between the hydroxyl group of the first-position carbon and the hydroxyl group of the fourth-position carbon of each monosaccharide, respectively (See Figure 5). A disaccharide can be composed of two molecules of the same sugar (e.g. maltose, which is composed of two D-glucose molecules linked via a glycosidic bond), or two different six-carbon sugars (e.g. lactose, which is D-glucose linked to D-galactose via a glycosidic bond). The nature of the glycosidic bonds is different between these two disaccharides; maltose is formed by an alpha glycosidic bond, whereas lactose is formed by a beta glycosidic bond. The alpha and beta designations of the glycosidic bonds refer to the configuration of the first-position carbon of the monosaccharide linked in a glycosidic bond. 

Polysaccharide Structure Depends on the Type of Glycosidic Bonds

Figure 6. Common polysaccharides. Plant starch (e.g. amylose) and glycogen are composed of alpha-D-glucose subunits linked through alpha glycosidic bonds. Starch is an unbranched polymer, whereas glycogen is branched, with 1 -> 6 linkages. Cellulose is composed of beta-D-glucose subunits linked through beta glycosidic bonds.

Polysaccharides are composed of linear chains of many molecules of glucose linked via glycosidic bonds (Figure 6). Glycogen and starch are composed of alpha-D-glucoses linked through alpha glycosidic bonds between carbons 1 and 4 of glucose (referred to as a 1 -> 4 linkage). In addition, some polysaccharides (e.g. glycogen) have additional alpha glycosidic bonds between carbons 1 and 6 of glucose (referred to as a 1 -> 6 linkage), resulting in a branched polysaccharide. In plants there are both branched and unbranched polysaccharides (e.g. amylopectin and amylose, respectively). Cellulose is an unbranched, long chain of glucose molecules linked by glycosidic bonds, however, the bonds are beta glycosidic bonds between carbons 1 and 4 of glucose. The resulting structure of cellulose is rigid and cellulose can aggregate to form microfibrils (a major component of the plant cell wall). Although both plant starch and cellulose are polymers of glucose, mammals can only use starch as a source of nutrition. Mammals lack the enzyme required to cleave the beta glycosidic bonds of cellulose, however, they do possess the enzymes that can cleave the alpha glycosidic bonds of starch. 

Lipids

Lipids are storage molecules and a major component of biological membranes

Lipids are a heterogeneous class of macromolecules, defined by their hydrophobic nature. Unlike the macromolecules described previously (proteins, nucleic acids and polysaccharides), lipids are not polymers of a repeating monomer. Lipids are a diverse group of molecules, composed predominantly of hydrocarbon (C-H) bonds. They have one common characteristic; they are insoluble in water. The most familiar lipids are the fats and oils we consume in the foods we eat. One important function of lipids is the storage of energy in the form of hydrocarbon bonds. Another critical function of lipids is the formation of membranes; all biological membranes are formed by the aggregation of lipids. Most lipids spontaneously aggregate when placed in water. This can be clearly seen when oil is mixed with water; the oil is not soluble in the water, therefore, it beads up to form droplets of oil. Finally, there are some lipids that function as lipid-soluble hormones, used as signals for intercellular communication.


Five Types of Important Lipids

Figure 7. Saturated and unsaturated fatty acids. The chemical composition and structure of two fatty acids, one saturated (palmitate) and one unsaturated (oleate), are shown. Note that the double bond in oleate causes a kink in the molecule. Carbon atoms are shown in black, hydrogen atoms are shown in blue, and oxygen atoms are shown in green.

There are five major types of lipids: fatty acids, triacylglycerols, phospholipids, terpenes and sterols. A fatty acidis a long, unbranched chain of hydrocarbons with a carboxyl (COOH) group at one end. The number of carbons varies amongst different fatty acids, and can range from 12 to 20 carbons. In addition, fatty acids vary in the number and position of double bonds between their carbons. Fatty acids without double bonds are referred to as saturated fatty acids. Fatty acids with only a few double bonds are referred to as unsaturated fatty acids. Fatty acids with many double bonds are referred to as polyunsaturated fatty acids. As illustrated in Figure 7, saturated fatty acids are linear molecules, whereas unsaturated molecules have a kink due to their double bonds.

A triacyglycerol (also called a triglyceride) is composed of three fatty acids linked to a glycerol molecule (see Figure 8). Triacylglycerols are commonly referred to as fats or oils, and are predominantly energy-storage molecules. This is the fat we try to "burn off" by exercise and restricting our diets. A triacylglycerol can contain three different fatty acids that vary in length and level of saturation. Animal fat (e.g. chicken fat) contains triacylglycerols with saturated fatty acids. Triacylglycerol derived from plants, which we commonly refer to as oils (e.g. corn oil, olive oil), contain many unsaturated fatty acids. The level of saturation of the fatty acids affects their state. Saturated fats (e.g. chicken fat) are semi-solid at room temperature, whereas unsaturated plant oils (e.g. olive oil) are liquid at room temperature. Saturated fatty acids can be packed together closely in a tight and orderly fashion. The kinked nature of unsaturated fatty acids prevents tight packing and results in a lower melting temperature for plant oils, therefore, they are liquid at room temperature. Partially hydrogenated fats (e.g. margarine) are derived from vegetable oils subjected to partial hydrogenation of the double bonds. 


Phospholipids, Terpenes and Sterols

Figure 8. Four types of lipids. The chemical structures of four different lipids are shown. A triacylglycerol, a phospholipid (phoshphotidylcholine), a sterol (cholesterol) and a terpene (geraniol).

Phospholipids are used predominantly in the formation of biological membranes. A phospholipid is similar to a triacylglycerol. It is composed of glycerol, two fatty acid chains, and a phosphate group that is also linked to a small polar group (see Figure 8 for an example). A phospholipid is amphipathic, having both polar and nonpolar regions. The highly polar "head" is comprised of the phosphate and polar group, and the long hydrophobic "tail" is comprised of the two fatty acid chains. When mixed with water, phospholipids spontaneously form a lipid bilayer. The lipid bilayer is two layers of phospholipids arranged in a tail-to-tail configuration, with their polar heads on the outside of the bilayer, in contact with water, and their hydrophobic tails pointing toward each other, shielded from the water. This feature makes them important to membrane structure. The properties of the lipid bilayer will be discussed in greater detail in Tutorial 4 (entitled Membrane Structure and Function). Phospholipids are a major component of biological membranes, where they comprise the bulk of the lipid bilayer.

Terpenes are comprised of long-chain hydrocarbons derived from a common, five-carbon subunit (see Figure 8for an example). Terpenes have diverse functions and include molecules such as carotenoid pigments and the visual pigment retinal (derived from vitamin A).

Sterols are structurally distinct from other lipids. Instead of long-chain hydrocarbons, sterols are composed of multiple, four-carbon, ring structures. Cholesterol (see Figure 8), which is a component of the plasma membrane of animal cells, is a sterol. Other sterol molecules include the hormones testosterone and estrogen.

Summary

This tutorial described the structures and properties of three families of macromolecules: nucleic acids, polysaccharides and lipids.

Nucleic acids are macromolecules that store, transmit and express the genetic information of a cell. DNA is the stored genetic material. RNA (mRNA, rRNA and tRNA) is involved in the expression of this information; the translation into protein. DNA and RNA are polymers of nucleotides linked via a phosphodiester bond. Nucleotides are composed of three functional groups: a sugar, a nitrogenous base and a phosphate group. The sugars in RNA are ribose, and in DNA are deoxyribose. Nucleotides in RNA contain the bases adenine and guanine (both purines), and cytosine and uracil (both pyrimidines). Nucleotides in DNA contain the bases adenine, guanine, cytosine and thymine (also a pyrimidine). DNA is double-stranded, and the two strands of DNA are held together by hydrogen bonds between the nitrogenous bases of complementary nucleotides. The complementary relationships between the nucleotides are as follows: adenine pairs with thymine (A-T base pair), and cytosine pairs with guanine (C-G base pair). The A-T base pair has two hydrogen bonds, and the G-C base pair has three. The structure of most double-stranded DNA is a right-handed double helix.

Polysaccharides are polymers of monosaccharides (simple sugars) linked via a glycosidic bond. They function in the cell as storage and structural molecules. Disaccharides are composed of two monosacchrides linked by a glycosidic bond. The most common polysaccharides are glycogen, starch and cellulose. All three are composed of long chains of D-glucose, but they differ in the configuration of glucose and the type of glycosidic bonds. Glycogen and plant starches (e.g. amylose) are composed of alpha-D-glucoses linked by alpha glycosidic bonds. Cellulose, a major component of the plant cell wall, is composed of long chains of beta-D-glucose linked by beta glycosidic bonds.

Lipids are a diverse group of molecules that are not polymers. Lipids are predominantly composed of hydrocarbons, and are distinguished by their hydrophobic nature. Fatty acids are unbranched, long-chain hydrocarbons. They vary in length and in number of double bonds. Saturated fatty acids do not have double bonds, whereas unsaturated fatty acids have some double bonds. Triacylgycerols are a class of lipids that store energy in the form of many carbon bonds. Triacylglycerols are composed of glycerol and three fatty acids. Phospholipids are a related class of lipids, composed of glycerol, two fatty acid chains, and a polar group such as a phosphate group. Phospholipids are distinguished by their dual nature (polar heads and hydrophobic tails) and their ability to form a lipid bilayer. Terpenes are long-chain hydrocarbons found in some plant pigments, as well as some animal visual pigments. Cholesterol, a sterol, is also a component of membranes. Sterols are a distinct class of lipids, characterized by a ringed-carbon structure.