The Structure of Nucleic Acids

7.2 The Structure of Nucleic Acids E X P E C TAT I O N S Describe and compare the molecular structure and function of DNA and RNA. Compare and contr...
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7.2

The Structure of Nucleic Acids

E X P E C TAT I O N S Describe and compare the molecular structure and function of DNA and RNA. Compare and contrast the arrangement of genetic material in prokaryotes and eukaryotes. Explain how changes in the molecular arrangement of genetic material are linked to particular stages in the cell cycle.

B

y the late 1940s, it was known that DNA was made up of a strand of nucleotides, and that each nucleotide was made up of a sugar, a phosphate group, and a particular nitrogenous base. Exactly how the strand was arranged, however, remained a mystery. The methodical work undertaken by British scientists Rosalind Franklin, pictured in Figure 7.9, and Maurice Wilkins to photograph and analyze X-ray diffraction images of DNA molecules added a number of new observations that helped other scientists to finally deduce the molecule’s structure.

structure — one pattern recurring at intervals of 0.34 nm, and another at intervals of 3.4 nm. As she prepared her samples for photographing, Franklin also observed how DNA reacted to water. From this evidence she deduced that the hydrophobic nitrogenous bases must be located on the inside of the helical structure, and that the hydrophilic sugar-phosphate backbone must be located on the outside, facing toward the watery nucleus of the cell. Her observations proved to be important keys to understanding the structure of DNA.

Figure 7.10 The shaded areas in this deceptively simple

image indicate the pattern formed by X rays as they diffract through crystallized DNA. This photograph was made by Rosalind Franklin in 1953, and provided a number of important clues about DNA’s molecular structure. Figure 7.9 Rosalind Franklin’s work was a major factor in the effort to determine the structure of DNA. Her contribution was not widely recognized at the time, in part because of prevailing attitudes toward women in science in the 1950s. Franklin died of cancer at age 38, shortly before the Nobel prize was awarded to Watson and Crick. Her many years of work with X rays may have contributed to her illness.

The pattern of shaded areas in the image shown in Figure 7.10, for example, indicated that DNA had a helical structure. From the nature of these X-ray “shadows,” Franklin was able to identify two distinct but regularly repeating patterns in the

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The partnership between the American geneticist James Watson and the British physicist Francis Crick was the first to produce a structural model of DNA that could account for all the experimental evidence at hand. Watson and Crick worked with physical models, as shown in Figure 7.11, trying different arrangements until they decided on the double-helix model that soon became established as the definitive structure for DNA. They published their results in a two-page paper in Nature magazine in 1953.

DNA — The Double Helix As you probably know, DNA is a thread-like molecule made up of two long strands of nucleotides bound together in the shape of a double helix. If the helix were unwound, the molecule would look something like a ladder, as shown in Figure 7.12. The sugar-phosphate “handrails” form the two sides, while the paired nitrogenous bases form the rungs. The space between the rungs is 0.34 nm, while the strand as a whole makes one complete turn of the helix for every 10 base pairs, or 3.4 nm. Thus, the structure accounts for the two different recurring patterns indicated by Franklin’s X-ray diffraction photograph. The following paragraphs explain how the nucleotides are joined within each

Figure 7.11 James Watson (left) and Francis Crick

in 1953 with their model of a DNA molecule.

G

C

sugar-phosphate “handrails”

T

A

T

A

C

G

C

G

hydrogen bonds between nitrogenous bases

T

A C

3.4 nm

T

3′

P 5′

3′

G

P 5′

C G A

5′

5′

3′

T

G 0.34 nm

A

5′

5′

G

C

P 3′

P

T A

T

T

T

A

A

P

3′

P

A 1 nm

P

3′

OH 3′ end

C P T

3′

5′

A P 3′

phosphate bridge

A DNA double helix

B DNA structure

Figure 7.12 The DNA molecule is made up of two chains

of nucleotides wound around each other. The “handrails” of the molecule are made up of alternating sugar and

P 5′ end

phosphate groups, with the phosphate groups serving as bridges between nucleotides. The nitrogenous bases protrude at regular intervals into the interior of the molecule.

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individual strand, how the two strands are bound together in the double helix, and how the molecule as a whole remains stable. Figure 7.12 shows both the primary and secondary structure of the DNA molecule. On each strand, the nucleotides are joined to form a long chain. The 5′ carbon of the pentose (five-carbon) sugar of one nucleotide is connected to the 3′ hydroxyl group on the next, with the phosphate group serving as a bridge between the two nucleotides. All the phosphate bridges have the same orientation, so each strand of DNA also has a specific orientation or directionality, which is opposite in direction to the other strand of the double helix. Thus each DNA strand (and any severed fragment of a DNA strand) has a 5′ and a 3′ end. By convention, the sequence of nucleotides along a strand of DNA is always read in the 5′ to 3′ direction. As Figure 7.12 also shows, the nitrogenous bases protrude at regular intervals from the sugarphosphate handrails into the interior of the DNA molecule. One of the challenges facing Watson and Crick was to determine how the bases could be arranged in such a way that the distance between the two handrails remained constant. They knew that the four bases fell into two different categories. Adenine and guanine are derived from the family of nitrogenous compounds known as purines, which have a double ring structure. Thymine and cytosine are derived from pyrimidines, which have a single ring structure. Watson and Crick hit upon the idea that if a purine always bonded with a pyrimidine, the base pairs would have a constant total width of three rings. It was not until after they had been experimenting with models for some time that Watson and Crick examined the molecular structure of the bases themselves. When they did so, they discovered that the structure of the bases allows only certain complementary base pairings: Adenine (A) can only form a stable bond with thymine (T), and cytosine (C) with guanine (G). The complementary bases are linked by hydrogen bonds, as shown in Figure 7.13. These pairings provided for the constant width of the molecule and, equally importantly, also supported Chargaff’s rule. Thus, wherever an A nucleotide appears on one DNA strand, a T must appear opposite it on the other, and wherever a C nucleotide appears on one strand, the other strand will have a G nucleotide.

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H N

N

N

H

N

sugar

O H

CH3

N

N

N O

Adenine (A)

sugar

Thymine (T)

H N

H

N

O

N

H

N

O

H

N

N

N sugar

N

Cytosine (C)

sugar

H Guanine (G)

Figure 7.13 Complementary base pairing in DNA. C-G pairs

are joined by three hydrogen bonds, while A-T pairs are joined by two hydrogen bonds.

In all, three kinds of forces contribute to the molecular stability of the DNA molecule. First, the phosphate bridges link the sugar-phosphate handrails. Second, hydrogen bonds between base pairs keep the two strands together in the helix. Finally, hydrophobic and hydrophilic reactions cause the bases to remain on the inside of the molecule and the handrails to face out into the watery nucleus of the cell. As illustrated in Figure 7.14, the two strands of DNA that make up each double helix are not identical but rather complementary to each other. The strands are also antiparallel — that is, the phosphate bridges run in opposite directions in each strand. This means that the end of each double-stranded DNA molecule contains the 5′ end of one strand and the 3′ end of the other. These two properties have important implications for DNA replication and protein synthesis, as discussed later in this chapter and in Chapter 8. You will have a chance to test your understanding of the composition of DNA and apply Chargaff’s rule in the Thinking Lab that follows. BIO FACT If you could arrange all the DNA strands contained in your body end to end, their total length would stretch 2 × 1010 km. This is well over 100 times the distance between Earth and the Sun.

5′ end

hydrogen bond

3′ end P

P T

A S

S P G

One pair of bases

P

C

phosphate 5′ end P 5′

S

S P

P

T

A S

S C

2′

P A

5′ end

Strand A

Strand B

THINKING

Strand A has the nucleotide sequence TGTCA. How would the sequence of strand B be written, according to convention?

LAB

Background Erwin Chargaff discovered that although the nucleotide composition of DNA varies from one species to another, that composition always follows certain rules. While the variation in nucleotides helps to explain the complexity of life, the physical structure of the DNA itself can also help certain organisms adapt to particular environments. Imagine you are working with a research team sampling the ocean floor near a hot vent that releases a steady stream of hot water. The hot water has a temperature of about 45°C, while the surrounding ocean has a temperature of 6°C.

adenine cytosine guanine thymine

C 2′

Figure 7.14 The two strands of DNA have complementary base sequences.

DNA Deductions

Nucleotide

C carbon numbering system 1′ C 3′

3′ end Ladder structure

5′

C 4′

S

S

4′

5′ C O P

T

S

deoxyribose

S

S

1′

P

P

G

A

base 3′

P

2′ 3′ T

1′

S

4′

3′ end

Presence in DNA of bacterial sample 1 (percent)

Presence in DNA of bacterial sample 2 (percent)

31

18

Your team collects two samples of bacteria — one from the mouth of the hot vent, and one from the ocean floor about 20 m away. When you return to the lab, you isolate the DNA from these bacteria to determine their nucleotide composition. The table shows the results of your test for the adenine content of the DNA.

You Try It Apply what you have learned about Chargaff’s findings and DNA composition to solve the following problems. 1. Complete the table to determine the amounts of the other nucleotides found in each DNA sample. 2. For each DNA sample, draw a linear stretch of DNA about 15 nucleotides long, with a nucleotide composition that corresponds to its data set. With a dotted line, illustrate the hydrogen bonds between complementary base pairs. 3. Considering the bonds between base pairs, which of these DNA samples is most likely taken from the bacteria collected at the mouth of the hot vent? Explain your answer.

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RNA Along with DNA, RNA is the other main nucleic acid. Both DNA and RNA are found in most bacteria and in eukaryotic cell nuclei. The molecular structure of RNA is similar to that of DNA, with three key differences. As Levene observed, the sugar component of RNA is ribose rather than deoxyribose. As noted previously, the nucleotide thymine is not found in RNA; in its place is the nucleotide uracil. RNA remains single stranded, although at times this single strand can fold back on itself to produce regions of complementary base pairs.

protein coat. Figure 7.16 shows the variety of forms that the genetic material of viruses can assume. Living cells face additional challenges in arranging their DNA — they have far more DNA than a virus, and the organization of this hereditary material must also allow for two key considerations. First, the material must be arranged in a compact manner to keep the long strands of DNA from interfering with one another or with other cellular processes. Second, the hereditary material of the organism must be protected from enzymes within the cell that are designed to break down free DNA into its component nucleotides. Prokaryotes and eukaryotes each have distinct ways of arranging their DNA to meet both requirements.

The different structures that may be assumed by the RNA molecule result in several different types of RNA, each serving a particular function. The specific structures and roles of these different molecules are described in more detail in Chapter 8.

Organization of Genetic Material So far, you have examined the primary structure of DNA — that is, the way in which nucleotides are joined together to form a chain. You have also looked at its secondary structure, in which the chain of nucleotides forms a stable double helix. How is this material organized in three-dimensional space within a cell? Although viruses are typically described as containing only a short strand of either DNA or RNA, this strand is still many hundreds of times longer than the virus itself (see Figure 7.15). This material must be arranged so that it fits within the

Figure 7.15 The protein coat of this virus has been broken,

enabling its single molecule of DNA to escape. In an intact virus, the entire length of the DNA molecule is packed within the head of the protein coat.

or

A The 5′ and 3′ ends of a DNA double helix can bind to each other, producing a closed loop.

B The double helix may remain as a linear strand.

C In some viruses, the genetic material is a molecule of RNA or of single-stranded DNA. In either case, this strand may form a closed loop or remain as a linear strand, and may show regions of complementary base pairing.

Figure 7.16 The relatively short strand of either DNA or RNA found in a virus

contains the information required to direct the infected cell to produce new viruses. As shown, this short strand can assume a variety of forms.

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Genetic Material in Prokaryotes Most prokaryotes have a single, double-stranded DNA molecule. One of the characteristic features of prokaryotes is that they have no nucleus. Therefore, there is no nuclear membrane to keep the DNA strand contained in a particular location within the cell. Instead, the prokaryote uses an arrangement that helps to pack genetic material tightly into a specific region known as the nucleoid or nuclear zone of the cell. To accomplish this, the ends of the DNA molecule bind together to form a closed belt. As shown in the photomicrograph and simplified illustration in Figure 7.17, this belt is then further twisted in on itself like a necklace that is coiled into a series of small loops. Such a structure is said to be supercoiled. The loops of the supercoiled DNA are held in place by proteins. In addition to the relatively large, supercoiled DNA molecule found in the nucleoid, prokaryotes often have one or more small, circular doublestranded DNA molecules floating free in the cytoplasm of the cell. These additional DNA molecules are called plasmids. Although plasmids are not physically part of the nucleoid DNA, these small strands of genetic material can contribute to cell metabolism and to the hereditary mechanism. For example, the genes that confer resistance to antibiotics may be found on plasmids rather than within the nucleoid DNA. Plasmids can be copied and transmitted between cells, or they can be incorporated into the cell’s nucleoid DNA and reproduced during cell division. As a result, the hereditary information contained on a plasmid can spread within bacterial colonies.

Plasmids have proven to be a valuable tool in genetic engineering techniques. You will learn more about the use of plasmids in DNA sequencing processes and in other applications later in this unit. Genetic Material in Eukaryotes Supercoiling is an effective way of arranging DNA within a prokaryote. However, even the simplest eukaryotic cell has over 10 times the DNA of a bacterial cell, and mammalian cells may have many thousands of times the quantity of genetic material found in a prokaryote. Each human cell nucleus contains about 2 m of DNA, or six billion base pairs. By way of comparison, this is roughly the equivalent of trying to pack 400 km of wet spaghetti into a bathtub — yet these DNA fibres never become entangled. A highly structured arrangement of proteins and DNA helps to pack and organize this material within the cell. The nuclei of plant and animal cells contain double-stranded DNA. This DNA is organized into a number of separate chromosomes. Each chromosome contains one linear double-stranded DNA molecule together with different types of the protein histone. Overall, the composition of a chromosome is about 60 percent protein, 35 percent DNA, and five percent RNA. These components are organized into the long fibres that Miescher called “nuclein,” and which are now known as chromatin. Figure 7.18 on the following page shows the arrangement of genetic material in a eukaryotic cell. The DNA molecule wraps tightly around groups of histone molecules in a regular pattern

Figure 7.17 The supercoiled molecule of bacterial DNA shown at left is coiled

into a series of small loops, as shown in the simplified illustration at right.

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to produce bead-like structural units called nucleosomes. Each nucleosome bead is a short segment of DNA (about 200 base pairs) wrapped twice around a cluster of eight histone molecules. The attraction between the acidic DNA and the highly alkaline histone molecules helps to keep the arrangement in place. A short stretch of DNA extends between each nucleosome, as shown in Figure 7.19. This short segment of DNA is bound to a single molecule of a type of histone known as H1. The interaction among H1 molecules helps to draw the arrangement into a tight, regular array. In turn, this array (which has a total thickness of about 30 nm) undergoes another level of packing.

It forms loops that attach to a supporting structure of non-histone proteins. As the cell prepares to reproduce, the protein structure folds back on itself to condense the chromatin even further. The result is the short, thick chromosomes you have seen in typical karyotypes. In a living cell, some regions of chromatin will be found in the 30 nm arrays during the bulk of the cell life cycle, while other regions are more condensed. You will learn more about the effect of this arrangement on cell functions in the next chapter. In the next section, you will learn about the processes involved in DNA replication and how they ensure the accurate transmission of hereditary material.

DNA double helix 2 nm

histone molecules

11 nm

A The DNA double helix winds around histone proteins to form a string of nucleosomes.

30 nm

B These nucleosomes form a regular, tightly packed array to produce lengths of chromatin fibre that are 30 nm wide.

H1 molecules

nucleosome

loops supporting protein structure

protein folding structure

300 nm

C Chromatin fibres form loops attached to a protein scaffold. Some chromatin fibres only assume this form as the cell prepares to divide, while other fibres remain in this looped structure throughout the life cycle of the cell.

700 nm

1400 nm condensed chromosome

D The supporting protein structure folds even further during mitosis to condense the genetic material into a short chromosome.

Figure 7.18 The successive ordering of genetic material within a eukaryotic cell.

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A

B

Figure 7.19 The total length of the DNA in a single human

chromosome reaches approximately 10 cm. The successive ordering of genetic material begins with the formation of nucleosomes (A) and culminates with the condensed chromosome (B), shown here as a pair of sister chromatids

SECTION

REVIEW

1.

K/U Describe the observations made by Franklin that proved to be keys to understanding the molecular structure of DNA.

2.

K/U Describe the evidence that led Watson and Crick to their particular model of DNA.

3.

K/U DNA is a large double helix, resembling a twisted ladder. Describe the component molecules that make up the ladder uprights and the pattern of their arrangement.

4.

Create a chart that compares and contrasts the similarities and differences in the structure of DNA and RNA.

5.

C The four nitrogenous bases are paired to make up the rungs of the DNA ladder. Differentiate between the purine and pyrimidine structures of each of these nitrogenous bases, and explain the significance of the pattern of their arrangement.

6.

K/U Watson and Crick concluded that DNA consisted of two individual strands arranged in antiparallel directions. Explain the significance of this arrangement.

7.

K/U Identify and describe the three different kinds of forces that contribute to the molecular stability of the DNA molecule.

8.

C

Describe the organization of genetic material in prokaryotic organisms. What purpose is served by having DNA incorporated into plasmids? K/U

during mitosis. This ordering compacts the DNA by a factor of tens of thousands — the equivalent of coiling 50 km of thread into a piece of rope that fits across the palm of your hand.

9.

K/U Describe the organization of DNA in eukaryotic organisms. What is the reason for the compact nature of chromosomes?

10.

I Scientists have extracted DNA from the different types of cells within one species and from the same kinds of cells among many different species. Decide whether the results from this research alone will or will not support the hypothesis that DNA is the genetic material. Justify your decision.

11.

K/U DNA is a doubled-stranded helical molecule. RNA is a single-stranded molecule. Based on the structural characteristics of each molecule, determine which is more efficient at coding genetic information.

12.

MC Should scientists be compelled to share information out of a spirit of fairness? Linus Pauling was one of the favoured competitors in the race to discover the molecular structure of DNA, due to his superior knowledge of organic chemistry. However, Watson and Crick, who had access to Franklin and Wilkins’ X-ray pictures and knowledge of Pauling’s theories from his son, claimed the victory. Based on your independent review of the history of this event, how do you think the race might have ended differently?

UNIT PROJECT PREP

Start gathering statistics on the type of cancer you have chosen to study. Who is most likely to be affected by this cancer?

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