Chapter 33: The Structure of Informational Macromolecules: DNA and RNA
The base name with the suffix "____" alone is a nucleotide, but with an unknown number of phosphoryl groups attached at an undesignated carbon atom of the sugar.
"ate,"
The structure of RNA differs from that of DNA in two respects:
(1) the sugar units in RNA are riboses rather than deoxyriboses and (2) one of the four major bases in RNA is uracil instead of thymine
1. One of the largest known DNA molecules is found in the 2. its genome is nearly as large as the human genome but is distributed among only __ chromosomes (Figure 33.10). 3. The largest of these chromosomes has strands of more than __ _______ base pairs. If such a DNA molecule could be fully extended, it would stretch more than ____ foot in length. (*Some plants contain even larger DNA molecules)
1. Indian muntjac, an Asiatic deer 2. 3 3. 1 billion 4. 1
The features of the Watson-Crick model of DNA are
1. Two helical DNA strands are coiled around a common axis, forming a right-handed double helix. The strands run in opposite directions; that is, they have opposite directionality. One strand has a 5′-to-3′ direction and pairs with the other strand, which has a 3′-to-5′ orientation. 2. The sugar-phosphate backbones are on the outside of the helix; therefore, the purine and pyrimidine bases lie on the inside. 3. The bases are nearly perpendicular to the helix axis, and adjacent bases are separated by approximately 3.4 Å. The helical structure repeats on the order of every 34 Å, with about 10.4 bases per turn of helix. There is a rotation of nearly 36 degrees per base (360 degrees per full turn/10.4 bases per turn). 4. The diameter of the helix is about 20 Å.
1. Two of the bases are derivatives of purine: 2. and two are derivatives of pyrimidine:
1. adenine and guanine 2. cytosine and thymine (DNA only) or uracil (RNA only)
1. Each groove is lined by...... 2. These interactions are essential for replication and transcription because
1. potential hydrogen-bond donor and acceptor atoms that enable interactions with proteins. 2. particular proteins bind to DNA, recognizing specific hydrogen-bond donors and acceptors on the surfaces of the grooves, to catalyze these processes
DNA molecules from higher organisms can be much larger. The human genome comprises approximately __ ________ base pairs distributed among ____ distinct DNA molecules—
3 billion; 24 (of different sizes)
There are about ____ m of DNA in each human cell, which are packaged into ____ chromosomes, all of which are in a nucleus that has a diameter of about. Clearly, the length of DNA and the size of the nucleus present a ________ problem.
3.6; 46; 5 μm; packaging
The backbones of the nucleic acids are formed by
3′-to-5′ phosphodiester linkages.
Most human cells have ___ _______ base pairs of information. All 6 billion base pairs would be ____ m in length if all of the molecules were laid end to end. Human beings are composed of approximately ____ _________ cells. If all of this DNA were strung end to end, it would reach to the sun and back about
6 billion; 3.6; 10 trillion; 65 times.
In each case, N-__ of a purine or N-___ of a pyrimidine is attached to the
9, 1, 1′-carbon atom (C-1′) of the sugar
A striking characteristic of naturally occurring DNA molecules is their length, because
A DNA molecule must comprise many nucleotides to carry the genetic information necessary for even the simplest organisms.
What is a stem-loop?
A nucleic acid structure, commonly seen in RNA, created when two complementary sequences within a single strand come together to form a double-helical structure, which constitutes the stem. The two strands of the stem are linked by the loop.
Compare and contrast A-DNA and B-DNA (look at Figure 33.17)
A-DNA, like B-DNA, is a right-handed double helix made up of antiparallel strands held together by Watson-Crick base-pairing. The A helix is wider and shorter than the B helix, and its base pairs are tilted rather than perpendicular to the helix axis
The Double Helix Facilitates the
Accurate Transmission of Hereditary Information
The Watson-and-Crick model of DNA is called
B-DNA.
Under physiological conditions, most DNA is in the ___ form. However, this structure is not the only one that DNA can form....
B; Studies of DNA revealed a different form called A-DNA, which appears when DNA is less hydrated.
How are base pairs placed in the double helix?
Base pairs are stacked nearly one on top of another in the double helix.
Major and minor groove sides:
Because the two glycosidic bonds are not diametrically opposite each other, each base pair has a larger side that defines the major groove and a smaller side that defines the minor groove
Nucleosomes are complexes of
DNA and Histones
Clearly, the nucleosome is just the first step in .
DNA compaction
The winding of DNA around the nucleosome core contributes to
DNA's packing by decreasing its linear extent. Wrapping this DNA around the histone octamer reduces the length to approximately 100 Å along the long dimension of the nucleosome. Thus, the DNA is compacted by a factor of 7. However, human chromosomes in metaphase, which are highly condensed, are compacted by a factor of 104.
What forms nucleosomes?
Eukaryotic DNA Wrapped Around Histones
The stacking of bases one on top of another also contributes to the stability of the double helix in two ways.
First, the double helix is stabilized by the hydrophobic effect: hydrophobic interactions between the bases drive the bases to the interior of the helix, resulting in the exposure of the more polar surfaces to the surrounding water. This arrangement is reminiscent of protein folding in which hydrophobic amino acids are interior in the protein and hydrophilic amino acids are exterior. Second, stacked bases attract one another through van der Waals forces (p. 21), a phenomenon called base stacking. Energies associated with van der Waals interactions are quite small, such that typical interactions contribute from 2 to 4 kJ mol−1 (0.5 to 1.0 kcal mol−1) per atom pair. In the double helix, however, a large number of atoms are in van der Waals contact, and the net effect, summed over these atom pairs, is substantial.
_____ major histones are present in chromatin:
Five; four histones, called H2A, H2B, H3, and H4, associate with one another; the other histone is called H1.
Histone ___ binds, in part, to the linker DNA.
H1
The Double Helix Is Stabilized by
Hydrogen Bonds and the Hydrophobic Effect
Contrast the major and minor grooves of the B form
In B-DNA, the major groove is wider (12 Å versus 6 Å) and deeper (8.5 Å versus 7.5 Å) than the minor groove
What are these double helices made up of?
In many cases, these double helices are made up entirely of Watson-Crick base pairs. In other cases, however, the structures include mismatched base pairs or unmatched bases that bulge out from the helix. Such mismatches destabilize the local structure but introduce deviations from the standard double-helical structure that can be important for higher-order folding and for function.
Brief discovery of the DNA double helix
James Watson and Francis Crick, using data obtained by Maurice Wilkins and Rosalind Franklin and simple molecular models, inferred a structural model for DNA that was the source of some remarkable insights into the functional properties of nucleic acids
What two people demonstrated that replication is semiconservative? How did they do it?
Meselson and Stahl. Matthew Meselson and Franklin Stahl carried out an ingenious experiment to establish this fundamental point. They labeled the parent DNA with 15N, a heavy isotope of nitrogen, to make it denser than ordinary DNA. The labeled DNA was generated by growing E. coli for many generations in a medium that contained 15NH4Cl as the sole nitrogen source. After the incorporation of heavy nitrogen was complete, the bacteria were abruptly transferred to a medium that contained 14N, the ordinary, lighter isotope of nitrogen. The question asked was: What is the distribution of 14N and 15N in the DNA molecules after successive rounds of replication? The distribution of 14N and 15N was revealed by the technique of density-gradient equilibrium sedimentation. A small amount of DNA was dissolved in a concentrated solution of cesium chloride having a density close to that of the DNA (1.7 g cm−3). This solution was centrifuged until it was nearly at equilibrium, where the opposing forces of sedimentation and diffusion created a gradient in the concentration of cesium chloride across the centrifuge tube. The result was a stable density gradient, ranging from 1.66 to 1.76 g cm−3. The DNA molecules in this density gradient were driven by centrifugal force into the region where the solution's density was equal to their own, yielding a narrow band of DNA that was detected by its absorption of ultraviolet light. 14N DNA and 15N DNA molecules in a control mixture differ in density by about 1%, enough to clearly distinguish the two types of DNA. DNA was then extracted from the bacteria at various times after they had been transferred from a 15N to a 14N medium and centrifuged. Analysis of these samples showed that there was a single band of DNA after one generation. The density of this band was precisely halfway between the densities of the 14N DNA and 15N DNA bands (Figure 33.16). The absence of 15N DNA indicated that parental DNA was not preserved as an intact unit after replication. The absence of 14N DNA indicated that all of the daughter DNA derived some of their atoms from the parent DNA. This proportion had to be half, because the density of the hybrid DNA band was halfway between the densities of the 14N DNA and 15N DNA bands. After two generations, there were equal amounts of two bands of DNA. One was hybrid DNA, and the other was 14N DNA. Meselson and Stahl concluded from these incisive experiments "that the nitrogen in a DNA molecule is divided equally between two physically continuous subunits; that following duplication, each daughter molecule receives one of these; and that the subunits are conserved through many duplications." Their results agreed perfectly with the Watson-Crick model for DNA replication
In the minor groove, what can serve as hydrogen acceptors?
N-3 of adenine or guanine and O-2 of thymine or cytosine can serve as hydrogen acceptors
In the major groove what are potential hydrogen acceptors?
N-7 of guanine or adenine is a potential acceptor, as are O-4 of thymine and O-6 of guanine.
Can the strands of the double helix be reversibly separated?
No
Damaging DNA Can Inhibit Cancer Cell Growth:
One means of combatting cancer is to modify DNA so as to prevent replication and transcription. Cisplatin is a chemotherapeutic agent that reacts with DNA such that nitrogens of adjacent purines replace the chloride atoms. This modification disrupts DNA structure and leads to cell death.
What yields these isolated beads?
Partial digestion of chromatin with DNAse, an enzyme that hydrolytically cleaves the phosphodiester backbone of the DNA, yields the isolated beads. These particles consist of fragments of DNA ≈200 bp in length bound to the eight histones. More extensive digestion yields a DNA fragment of 145 bp bound to the histone octamer. This smaller complex of the histone octamer and the 145-bp DNA fragment is the nucleosome core particle.
Eukaryotic DNA Is Associated with Specific
Proteins
How is such a regular structure able to accommodate an arbitrary sequence of bases, given the different sizes and shapes of the purines and pyrimidines? We will see the implications of this below and in Chapter 34. The base-pairing also helps to stabilize the double helix.
Restricting the combinations in which bases on opposite strands can be paired—A with T and C with G—alleviates this problem. When guanine is paired with cytosine and adenine with thymine to form base pairs, these pairs have essentially the same shape (Figure 33.12). These base pairs, often called Watson-Crick base pairs, are held together by hydrogen bonds. These base-pairing rules mean that, if the sequence of one strand is known, the sequence of the other strand is defined.
The Major and Minor Grooves Are Lined by
Sequence-Specific Hydrogen-Bonding Groups
DNA and RNA Differ in the
Sugar Component and One of the Bases
Double-Stranded DNA Can Wrap Around Itself to Form
Supercoiled Structures
__________ contributes to the compaction of DNA.
Supercoiling
How do DNA and RNA strands have directionality?
The 5′ end will often have a phosphoryl group attached to the 5′-OH group. One end of the strand has a free 5′-OH group (or a 5′-OH group attached to a phosphoryl group), whereas the other end has a 3′-OH group, and neither end is linked to another nucleotide. By convention, the base sequence is written in the 5′-to-3′direction. Thus, the symbol ACG indicates that the phosphorylated or unlinked 5′-OH group is on deoxyadenylate (or adenylate), whereas the unlinked 3′-OH group is on deoxyguanylate (or guanylate). Because of this directionality, ACG and GCA correspond to different compounds.
Example of topological structure
The Mobius strip, which has only one side, is an example of a topological structure. The Dutch graphic artist M. C. Escher illustrated the unique property of the Mobius strip by depicting ants crawling along the strip, always returning to the starting point after having traversed every part of the strip on both sides without ever crossing an edge.
In the major groove what are potential hydrogen donors?
The amino groups attached to C-6 of adenine and C-4 of cytosine can serve as hydrogen donors.
What two things immediately suggest how the genetic material might replicate? Explain and look at Figure 33.14!
The double-helical model of DNA and the presence of specific base pairs. The sequence of bases of one strand of the double helix precisely determines the sequence of the other strand. Thus, the separation of a double helix into its two component strands would yield two single-stranded templates onto which new double helices could be constructed, each of which would have the same sequence of bases as the parent double helix. Consequently, as DNA is replicated, one of the strands of each daughter DNA molecule would be newly synthesized, whereas the other would be passed unchanged from the parent DNA molecule. This distribution of parental atoms is achieved by semiconservative replication.
What is chromatin
The entire complex of a cell's DNA and associated protein; chromatin is essentially isolated chromosomes, although the exact relation between the two remains to be determined.
One of the reasons for DNA's use rather than RNA as the hereditary material in all modern cells and in many viruses.
The greater stability of DNA
What also lies in the major groove?
The methyl group of thymine also lies in the major groove.
What is the next step? In one model, the nucleosomes are packed into two interwound left-handed helical stacks. The linker DNA connects successive nucleosomes, crossing the interior of the fiber (Figure 33.27). The folding of these fibers of nucleosomes into loops further compacts DNA
The nucleosomes themselves are arranged in 30-nm fibers. The nature of the arrangement is under investigations, and more than one arrangement is likely. nucleosomes are arranged into two interwound left-handed helical stacks, with the linker DNA crossing the interior of the fiber. Further folding generates the chromosome. The folding of these fibers of nucleosomes into loops further compacts DNA
Why are supercoiling and nucleosome formation important for the structure of DNA in a cell?
They help COMPACT the DNA
Can DNA double helices adopt multiple forms?
Yes
Explain Z-DNA
Z-DNA Is a Left-Handed Double Helix in Which Backbone Phosphoryl Groups Zigzag: A third type of double helix is left-handed, in contrast with the right-handed screw sense of the A and B helices. Furthermore, the phosphoryl groups in the backbone are zigzagged; hence, this form of DNA is called Z-DNA. Although the biological role of Z-DNA is still under investigation, Z-DNA-binding proteins, which have a highly conserved Z-DNA binding domain, are found in many organisms including humans.
Supercoiling is a property not only of circular DNA. It also applies to linear DNA molecules that have
a constrained configuration, such as when DNA is packaged into chromosomes (Section 33.4).
The existence of Z-DNA shows that DNA is
a flexible, dynamic molecule whose parameters are not as fixed as depictions suggest.
Histones have strikingly basic properties because
a quarter of the residues in each histone are either arginine or lysine.
To prevent the strain induced by overwinding,
a specialized set of enzymes is present to introduce supercoils that favor strand separation
The base lies _____ the plane of the sugar when the structure is written in the standard orientation; that is, the configuration of the N-________ linkage is β.
above; glycosidic
The nucleoside units in RNA are called
adenosine, guanosine, cytidine, and uridine.
This renaturation process is sometimes called
annealing.
For example, the DNA of a virus such as polyoma, which can cause ______ in certain organisms, is _____ nucleotides in length.
cancer; 5100
DNA replication is the basis of
cell duplication, growth, and, ultimately, reproduction.
The final DNA-protein complex is called a
chromosome
A supercoiled DNA molecule has a more _______ shape than that of its relaxed counterpart.
compact
DNA molecules inside cells necessarily have a very __ _________ shape.
compact
The amino acid sequences of histones, including their amino-terminal tails, are remarkably ________ from yeast through human beings
conserved
The backbone is _________ in DNA and RNA, but the bases
constant; vary from one monomer to the next.
The four nucleoside units in DNA are called
deoxyadenosine, deoxyguanosine, deoxycytidine, and thymidine.
In regard to DNA, the trinucleotide consists of
deoxyadenylate monophosphate, deoxycytidylate monophosphate, and deoxyguanylate monophosphate joined together by phosphodiester linkages, in which "p" denotes a phosphoryl group.
The sugar in deoxyribonucleic acid (DNA) is
deoxyribose.
Note that the major groove displays more features that
distinguish one base pair from another than does the minor groove.
Nucleic Acid Strands Can Form a _________-_________ Structure
double helical
As we have seen, DNA is usually not a simple helix but is compacted into a more complex structure. Even single-stranded nucleic acids, most commonly RNA, often fold back on themselves to form well-defined and often complex structures. These complex structures allow RNA to perform a host of functions that the
double-stranded DNA molecule cannot
If the A helix were simply a property of dehydrated DNA, it would be of little significance. However,
double-stranded regions of RNA and at least some RNA-DNA hybrids adopt a double-helical form very similar to that of A-DNA.
RNA Can Adopt _______ Structures
elaborate
What ways other than supercoiling exist to compact the large amount of DNA in a eukaryotic nucleus?
further compaction is attained with the assistance of certain proteins.
In fact, histones constitute _____ the mass of a eukaryotic chromosome.
half
In the laboratory, the two strands of the double helix can be separated by
heating a solution of DNA. The thermal energy causes the DNA molecules to move to such a degree that the weak forces holding the helix together, such as the hydrogen bonds between the bases, break apart.
Eukaryotic DNA is tightly bound to a group of small basic proteins called
histones.
The absence of the 2′-hydroxyl group in DNA further increases its resistance to
hydrolysis.
In the presence of nucleophilic species, a 2′-hydroxyl group would
hydrolyze the phosphodiester linkage and cause a break in the nucleic acid backbone.
As stated earlier, the base sequence is the ______ _______ of nucleic acids.
information content
The larger size of the major groove in B-DNA makes it more accessible for
interactions with proteins that recognize specific DNA sequences.
When chromatin is stretched out so that the DNA and associated nucleosomes can be seen by an electron microscope,
it has the appearance of beads on a string; each bead has a diameter of approximately 100 Å (Figure 33.24).
When does dissociation of the double helix occur?
it occurs relatively abruptly at a certain temperature.
Figure 33.16: The detection of semiconservative replication of E. coli DNA by density-gradient centrifugation: The position of a band of DNA depends on
its content of 14N and 15N. After 1.0 generation, all of the DNA molecules were hybrids containing equal amounts of 14N and 15N
The DNA forms a ______-______ _______ as it wraps around the outside of the histone octamer. The protein core forms contacts with
left-handed superhelix; the inner surface of the superhelix at many points, particularly along the phosphodiester backbone and the minor groove of the DNA.
The DNA molecules in human chromosomes are ______, while DNA molecules from some other organisms are
linear; circular
DNA and RNA are macromolecules that are ______ polymers built up from _____ units connected end to end. Each monomer unit within the polymer consists of components:
linear; similar; three; a sugar, a phosphate, and a base.
The DNA connecting core particles in undigested chromatin is called
linker DNA (Figure 33.25).
Histone H1, which has a different structure from that of the other histones, seals off the nucleosome at the location at which the
linker DNA enters and leaves the nucleosome.
Nucleosome core particles are joined to one another by
linker DNA.
The separation of the two strands of DNA in replication requires
local unwinding of the double helix.
Ribonucleic acid (RNA), like DNA, is a
long unbranched polymer consisting of nucleotides joined by 3′ → 5′ phosphodiester linkages (Figure 33.4).
DNA Molecules Are Very ______ and Have
long; Directionality
The dissociation of the double helix is called
melting or denaturation
Note that each phosphodiester linkage in the backbone of both DNA and RNA has a ________ charge. What does this charge do?
negative; This negative charge repels nucleophilic species such as hydroxide ion, which are capable of hydrolytically cleaving the phosphodiester linkages of the nucleic acid backbone. This resistance is crucial for maintaining the integrity of information stored in nucleic acids.
Most naturally occurring DNA molecules are _______ supercoiled. What is the basis for this prevalence?
negatively; Negative supercoiling arises from the unwinding or underwinding of the DNA. In essence, negative supercoiling prepares DNA for processes requiring separation of the DNA strands, such as replication or transcription. Positive supercoiling condenses DNA as effectively, but it makes strand separation more difficult.
The sequence of bases uniquely characterizes a ________ ________ and is a form of linear information.
nucleic acid
A more precise nomenclature also is commonly used. A compound formed by the attachment of a phosphoryl group to C-5′ of a nucleoside sugar (the most common site of phosphate esterification) is called a
nucleoside 5′-phosphate or a 5′-nucleotide.
A nucleotide is a
nucleoside joined to one or more phosphoryl groups by an ester linkage and is most commonly referred to as a nucleoside with the number of attached phosphoryl groups noted. For instance, a nucleoside monophosphate is a nucleotide.
The four nucleotide units that link to form DNA are
nucleoside monophosphates called deoxyadenylate, deoxyguanylate, deoxycytidylate, and thymidylate.
A unit consisting of a base bonded to a sugar is referred to as a
nucleoside.
What are the mimetic units of nucleic acids?
nucleotides
indeed, the complexity of some RNA molecules rivals that of proteins, and these RNA molecules perform a number of functions that had formerly been thought to be the exclusive role of proteins. For instance,
one of the RNA components of ribosomes—a large complex of RNAs and proteins on which proteins are synthesized—is the actual catalyst for protein synthesis
Syn and anti refer to the
orientation of the N-glycosidic bond between the base and deoxyribose. In the syn orientation, the base is above the deoxyribose. Pyrimidines can be in anti orientations only, whereas purines can be anti or syn.
What abbreviated notations denote a trinucleotide?
pApCpG, pACG, or, most commonly, ACG
The sugars in nucleic acids are linked to one another by __________ ________. Explain this in specifics
phosphodiester bridges. Specifically, the 3′-hydroxyl (3′-OH) group of the sugar component of one nucleotide is bonded to a phosphoryl group, and the phosphoryl group is, in turn, joined to the 5′-hydroxyl group of the adjacent sugar, forming a phosphodiester linkage.
The structure of a DNA strand: The strand has a 5′ end, which is usually attached to a ______ _______, and a 3′ end, which is usually a free ______ ______
phosphoryl group; hydroxyl group.
Chromatin is made up of
repeating units, each containing 200 bp of DNA and two copies each of H2A, H2B, H3, and H4, called the histone octamer. These repeating units are known as nucleosomes.
RNA: The simplest and most common structural motif formed is a _____-______, created when
stem-loop; two complementary sequences within a single strand come together to form a double-helical structure (Figure 33.30).
Bacterial chromosomes must employ a new structural property to fit in the cell. The axis of the double helix can itself be twisted into a superhelix, a process called
supercoiling
The "deoxy" prefix refers to the fact that
the 2′-carbon atom of the sugar lacks the oxygen atom that is linked to the 2′-carbon atom of ribose (the sugar in ribonucleic acid, or RNA)
Replication depends on
the ability of the bases found in nucleic acids to form specific base pairs in such a way that a helical structure consisting of two strands is formed.
In the minor groove, what can serve as a hydrogen donor?
the amino group attached to C-2 of guanine can be a hydrogen donor
The strand of sugars linked by phosphodiester bridges is referred to as
the backbone of the nucleic acid (Figure 33.4).
The nucleic acids DNA and RNA are well suited to functioning as
the carriers of genetic information by virtue of their structures.
Explain this formation in more detail:
the eight histones in the core particle are arranged into an (H3)2(H4)2 tetramer and a pair of H2A-H2B dimers (Figure 33.26). The tetramer and dimers come together to form a complex around which the DNA wraps. In addition, each histone has an amino-terminal tail that extends out from the core structure. These tails are flexible and contain a number of lysine and arginine residues. As we shall see, covalent modifications of these tails play an essential role in modulating the accessibility of DNA for transcription
Other features of nucleic acid structure facilitate the process of replication—that is,
the generation of two copies of a nucleic acid from one.
An examination of the DNA molecule in the B form, as shown in Figure 33.17, reveals the presence of two distinct grooves, called the major groove and the minor groove. These grooves arise because
the glycosidic bonds of a base pair are not diametrically opposite each other
Single-stranded nucleic acids can adopt structures more complex than simple stem-loops through
the interaction of more widely separated bases. Often, three or more bases interact to stabilize these structures. In such cases, hydrogen-bond donors and acceptors that do not participate in Watson-Crick base pairs form hydrogen bonds in nonstandard pairings (Figure 33.31). Metal ions such as magnesium ion (Mg2+) often assist in the stabilization of these more elaborate structures.
This local unwinding must lead either to
the overwinding of surrounding regions of DNA or to supercoiling.
The melting temperature Tm is defined as
the temperature at which half the helical structure is lost. Strands can also be separated by adding acid or alkali to ionize the nucleotide bases and disrupt base-pairing.
Separated complementary strands of nucleic acids spontaneously reassociate to form a double helix when
the temperature is lowered below Tm.
During DNA replication and transcription,
the two strands of the double helix must be separated from one another, at least in a local region. In other words, sometimes the archival information must be accessible to be useful.
What accounts for nucleic acids' ability to carry information in the form of a sequence of bases?
their covalent structure
Note that thymidine contains deoxyribose; however, by convention, the prefix "deoxy" is not added, because
thymine-containing nucleotides are found only rarely in RNA.
The unwound DNA and the supercoiled DNA are
topological isomers, or topoisomers; that is, they have the same sequence but have different structures because of differences in the coiling of the DNA molecules (Figure 33.23).
The study of DNA structures has been enriched by a branch of mathematics called ______, which deals with
topology, structural properties unchanged by deformations such as stretching and bending.
Nucleoside ___phosphates are the monomers—the building blocks—that are linked to form RNA and DNA.
tri
What is the structural consequence of unwinding before ligation?
two limiting conformations are possible. First, the DNA can fold into a structure containing 23 turns of B helix and an unwound loop (Figure 33.22D). However, bases in the loop do not form base pairs, and base pairs stabilize the double helix; so this structure is somewhat unstable. The second structural possibility is for the DNA to adopt a supercoiled structure with 23 turns of B helix and 2 turns of right-handed (termed negative) superhelix (Figure 33.22E). In the superhelix, no bases are left unpaired.
The E. coli genome is a single DNA molecule consisting of
two strands of 4.6 million nucleotides
The stacked bases interact with
van der Waals forces. Such stacking forces help stabilize the double helix.