1. Chapter Nine Nucleic Acids: How Structure Conveys Information

2. Chapter Outline
9-1 Levels of Structure in Nucleic Acids 9-2 The Covalent Structure of Polynucleotides 9-3 The Structure of DNA 9-4 Denaturation of DNA 9-5 The Principal Kinds of RNA and Their Structures

3. Nucleic Acids Levels of structure
1°structure: the order of bases on the polynucleotide sequence; the order of bases specifies the genetic code
2°structure: the three-dimensional conformation of the polynucleotide backbone
3°structure: supercoiling
4°structure: interaction between DNA and proteins

4. Covalent Structure of Polynucleotides
Nucleic acid: a biopolymer containing three types of monomer units
a base derived from purine or pyrimidine (nucleobases)
a monosaccharide, either D-ribose or 2-deoxy-D-ribose
phosphoric acid
RNA (Ribonucleic Acid)
DNA (Deoxyribonucleic Acid)

5. Pyrimidine/Purine Bases
The structures of pyrimidine and purine are shown here for comparison
Figure 9.1 Structures of the common nucleobases.
The structures of pyrimidine and purine
are shown for comparison.

6. Other Bases Less common bases can occur
Principally but not exclusively, in transfer RNAs
Figure 9.2 Structures of some of the less common
nucleobases. When hypoxanthine is bonded
to a sugar, the corresponding compound is called
inosine.

7. Nucleosides
Nucleoside: a compound that consists of D-ribose or 2-deoxy-D-ribose covalently bonded to a nucleobase by a -N-glycosidic bond
Lacks phosphate group
Figure 9.3 A comparison of the structures
of a ribonucleoside and a deoxyribonucleoside.
(A nucleoside does not have a phosphate group
in its structure.)

8. Nucleotides
Nucleotide: a nucleoside in which a molecule of phosphoric acid is esterified with an -OH of the monosaccharide, most commonly either the 3’-OH or the 5’-OH
Name based on parent nucleoside with a suffix “monophosphate”
Polymerization leads to nucleic acids. Linkage is repeated (3’,5’-phosphodiester bond)
(Biochemical Connections p. 232)
Figure 9.4 The structures and names of the
commonly occurring nucleotides. Each nucleotide
has a phosphate group in its structure. All structures
are shown in the forms that exist at pH 7.

9. DNA - 1° Structure
Deoxyribonucleic acids, DNA: a biopolymer that consists of a backbone of alternating units of 2-deoxy-D-ribose and phosphate
the 3’-OH of one 2-deoxy-D-ribose is joined to the 5’-OH of the next 2-deoxy-D-ribose by a phosphodiester bond
Primary Structure: the sequence of bases along the pentose-phosphodiester backbone of a DNA molecule
base sequence is read from the 5’ end to the 3’ end
System of notation single letter (A,G,C,U and T)

10. DNA differs from RNA Sugar is 2’-deoxyribose, not ribose.
• Sometimes “d” used to designate “deoxy”
• Writing a DNA strand
an abbreviated notation
even more abbreviated notations
d(GACAT)
pdApdCpdGpdT pdACGT
Figure 9.5 A fragment of an RNA chain.
Figure 9.6 A portion of a DNA chain.

11. DNA - 2° Structure
Secondary structure: the ordered arrangement of nucleic acid strands
the double helix model of DNA 2°structure was proposed by James Watson and Francis Crick in 1953
Double helix: a type of 2° structure of DNA molecules in which two antiparallel polynucleotide strands are coiled in a right-handed manner about the same axis
structure based on X-Ray crystallography
Figure 9.7 The double helix A complete turn of the helix spans ten base pairs, covering a distance of 34 Å (3.4 nm). The individual base pairs are spaced 3.4 Å (0.34 nm) apart. The places where the strands cross hide base pairs that extend perpendicular to the viewer. The inside diameter is 11 Å (1.1 nm), and the outside diameter is 20 Å (2.0 nm). Within the cylindrical outline of the double helix are two grooves, a small one and a large one. Both are large enough to accommodate polypeptide chains. The minus signs alongside the strands represent the many negatively charged phosphate groups along the entire length of each strand.

12. Base Pairing Base pairing is complimentary
A major factor stabilizing the double helix is base pairing by hydrogen bonding between T-A and between C-G
T-A base pair comprised of 2 hydrogen bonds
G-C base pair comprised of 3 hydrogen bonds
Figure 9.8 Base pairing. The adenine–thymine
(A—T) base pair has two hydrogen bonds,
whereas the guanine–cytosine (G—C) base pair
has three hydrogen bonds. Hydrogen bonds are
shown as red vertical lines.

13. Other Forms of DNA considered the physiological form
B-DNA
considered the physiological form
a right-handed helix, diameter 11Å
10 base pairs per turn (34Å) of the helix
A-DNA
a right-handed helix, but thicker than B-DNA
11 base pairs per turn of the helix
has not been found in vivo
Z-DNA
a left-handed double helix
may play a role in gene expression

14. Comparison of A,B, and Z forms of DNA
• Both A and B-DNA are right-handed helices
• Z-DNA is left handed
• Z-DNA occurs in nature, usually consists of alternating purine-pyrimidine bases
• Methylated cytosine found also in Z-DNA
Figure 9.9 Comparison of the A, B, and Z forms of DNA. In the A form, the base pairs have a marked propeller twist
with respect to the helix axis. In the B form, the base pairs lie in a plane that is close to perpendicular to the helix
axis. Z-DNA is a left-handed helix and in this respect differs from A-DNA and B-DNA, both of which are right-handed
helices. (Robert Stodala, Fox Chase Cancer Research Center. Illustration, Irving Geis. Rights owned by Howard Hughes Medical
Institute. Not to be reproduced without permission.)

15. Other Features of DNA Base stacking
bases are hydrophobic and interact by hydrophobic interactions
in standard B-DNA, each base rotated by 32° compared to the next and, while this is perfect for maximum base pairing, it is not optimal for maximum overlap of bases; in addition, bases exposed to the minor groove come in contact with water
many bases adopt a propeller-twist in which base pairing distances are less optimal but base stacking is more optimal and water is eliminated from minor groove contacts

16. Z-form is derivative of B-form
Produced by flipping one side of the backbone 180˚ without disturbing the backbone covalent bonds or hydrogen bonds
Figure 9.11 Formation of Z-DNA. A Z-DNA section can form in the middle of a section of
B-DNA by rotation of the base pairs, as indicated by the curved arrows.

17. Helical/Propeller Twists
Bases that are exposed to minor groove contact with water
They twist in a “propeller twist” fashion
Results in:
• less optimal base pair distance
• More optimal base pair stacking (eliminates presence of water molecules)
Figure 9.12 Helical twists. Two base pairs
with 32° of right-handed helical twist; the minorgroove
edges are drawn with heavy shading.
Figure 9.13 Propeller-twisted base pairs. Note
how the hydrogen bonds between bases are
distorted by this motion, yet remain intact. The
minor-groove edges of the bases are shaded.

18. DNA - 3° Structure
Tertiary structure: the three-dimensional arrangement of all atoms of a nucleic acid; commonly referred to as supercoiling
Circular DNA: a type of double-stranded DNA in which the 5’ and 3’ ends of each stand are joined by phosphodiester bonds
Supercoiling- Further coiling and twisting of DNA helix.
Topoisomerases
Class I: cut the phosphodiester backbone of one strand, pass the end through, and reseal
Class II: cut both strands, pass some of the remaining DNA helix between the cut strands, and reseal
DNA gyrase: a bacterial topoisomerase

19. Super DNA Coiled Topology
Prokaryotic DNA is circular. It can form supercoils.
• Double helix can be considered to a 2-stranded, right handed coiled rope
Can undergo positive/negative supercoiling
Figure 9.14 Supercoiled DNA topology. The
DNA double helix can be approximated as a
two-stranded, right-handed coiled rope. If one
end of the rope is rotated counterclockwise, the
strands begin to separate (negative supercoiling).
If the rope is twisted clockwise (in a right-handed
fashion), the rope becomes overwound (positive
supercoiling). Get a piece of right-handed multistrand
rope, and carry out these operations to
convince yourself. (Based on Pennisi, E. (2006).
Science 312(5779), 1467–68. Copyright © 2015
Cengage Learning®.)

20. DNA Gyrase is a bacterial topoisomerase
Figure 9.15 A model for the action of bacterial
DNA gyrase (topoisomerase II).

21. Chromatin • The structure of chromatin • Each “Bead” is a nucleosome
• Nucleosome consists of: DNA wrapped around histone core
• Recent research has shown that structure and spacing of nucleosomes is important in chromatin function.
Figure 9.16 The structure of chromatin. DNA
is associated with histones in an arrangement that
gives the appearance of beads on a string. The
“string” is DNA, and each of the “beads” (nucleosomes)
consists of DNA wrapped around a protein
core of eight histone molecules. Further coiling
of the DNA spacer regions produces the compact
form of chromatin found in the cell.
Figure 9.17 The rate of mutation surrounding nucleosomes
is not constant. Substitution mutations peak in the nucleosomes
themselves, and are at a low point in the linker regions. Conversely,
insertion and deletion mutations (indel in the figure) are the opposite.
Researchers are attempting to establish why this is. (From Semple, C. A.,
and Taylor, M. S. (2009). Molecular biology: The structure of change.
Science 323, 347–348. Reprinted with permission from AAAS.)

22. Chromatin Figure 9.16 The structure of chromatin. DNA
is associated with histones in an arrangement that
gives the appearance of beads on a string. The
“string” is DNA, and each of the “beads” (nucleosomes)
consists of DNA wrapped around a protein
core of eight histone molecules. Further coiling
of the DNA spacer regions produces the compact
form of chromatin found in the cell.
Figure 9.17 The rate of mutation surrounding nucleosomes
is not constant. Substitution mutations peak in the nucleosomes
themselves, and are at a low point in the linker regions. Conversely,
insertion and deletion mutations (indel in the figure) are the opposite.
Researchers are attempting to establish why this is. (From Semple, C. A.,
and Taylor, M. S. (2009). Molecular biology: The structure of change.
Science 323, 347–348. Reprinted with permission from AAAS.)

23. Supercoiling in Eukaryotic DNA
Histone: a protein, particularly rich in the basic amino acids Lys and Arg; found associated with eukaryotic DNA
five main types: H1, H2A, H2B, H3, H4
Chromatin: DNA molecules wound around particles of histones in a beadlike structure
Topological changes induced by supercoiling accommodated by histone-protein component of chromatin.

24. Denaturation of DNA Denaturation: disruption of 2° structure
most commonly by heat denaturation (melting)
as strands separate, absorbance at 260 nm increases
increase is called hyperchromicity
midpoint of transition (melting) curve = Tm
the higher the % G-C, the higher the Tm
renaturation is possible on slow cooling
Figure 9.18 The experimental determination
of DNA denaturation. This is a typical meltingcurve
profile of DNA, depicting the hyperchromic
effect observed on heating. The transition (melting)
temperature, Tm, increases as the guanine and
cytosine (the G!C content) increase. The entire
curve would be shifted to the right for a DNA
with higher G!C content and to the left for a
DNA with lower G!C content.

25. Denaturation of DNA Double helix unwinds when DNA is denatured
Can be re-formed with slow cooling and annealing
Figure 9.19 Helix unwinding in DNA denaturation.
The double helix unwinds when DNA
is denatured, with eventual separation of the
strands. The double helix is re-formed on renaturation
with slow cooling and annealing.

26. Principal Kinds of RNA RNA
consist of long, unbranched chains of nucleotides joined by phosphodiester bonds between the 3’-OH of one pentose and the 5’-OH of the next
the pentose unit is -D-ribose (it is 2-deoxy-D-ribose in DNA)
the pyrimidine bases are uracil and cytosine (they are thymine and cytosine in DNA)
in general, RNA is single stranded (DNA is double stranded)

27. Information Transfer in Cells
Information encoded in the nucleotide sequence of DNA is transcribed through RNA synthesis
Sequence then dictated by DNA sequence
Central dogma of biology
Figure 9.20 The fundamental process of
information transfer in cells. (1) Information
encoded in the nucleotide sequence of DNA is
transcribed through synthesis of an RNA molecule
whose sequence is dictated by the DNA sequence.
(2) As the sequence of this RNA is read (as groups
of three consecutive nucleotides) by the protein
synthesis machinery, it is translated into the
sequence of amino acids in a protein. This information
transfer system is encapsulated in the
dogma DNA → RNA → protein.

28. mRNA in Transcription
Figure 9.21 The role of mRNA in transcription. The properties of mRNA molecules in prokaryotic
versus eukaryotic cells during transcription and translation.

29. RNA
RNA molecules are classified according to their structure and function

30. tRNA Transfer RNA, tRNA: the smallest kind of the three RNAs
a single-stranded polynucleotide chain between nucleotide residues
carries an amino acid at its 3’ end
intramolecular hydrogen bonding occurs in tRNA
Figure 9.22 The cloverleaf depiction of transfer
RNA. Double-stranded regions (shown in red)
are formed by folding the molecule and stabilized
by hydrogen bonds between complementary base
pairs. Peripheral loops are shown in yellow. There
are three major loops (numbered) and one minor
loop of variable size (not numbered).
Figure 9.23 Structures of some modified
bases found in transfer RNA. Note that the
pyrimidine in pseudouridine is linked to ribose
at C-5 rather than at the usual N-1.

31. rRNA
Ribosomal RNA, rRNA: a ribonucleic acid found in ribosomes, the site of protein synthesis
only a few types of rRNA exist in cells
ribosomes consist of 60 to 65% rRNA and 35 to 40% protein
in both prokaryotes and eukaryotes, ribosomes consist of two subunits, one larger than the other
analyzed by analytical ultracentrifugation
particles characterized by sedimentation coefficients, expressed in Svedberg units (S)
Figure 9.25 The analytical ultracentrifuge.
(a) Top view of an ultracentrifuge rotor. The solution
cell has optical windows; the cell passes through a light
path once each revolution. (b) Side view of an ultracentrifuge
rotor. The optical measurement taken as the
solution cell passes through the light path makes it possible
to monitor the motion of sedimenting particles.

32. mRNA
Messenger RNA, mRNA: a ribonucleic acid that carries coded genetic information from DNA to ribosomes for the synthesis of proteins
present in cells in relatively small amounts and very short-lived
single stranded
biosynthesis is directed by information encoded on DNA
a complementary strand of mRNA is synthesized along one strand of an unwound DNA, starting from the 3’ end

33. snRNA Small nuclear RNA (snRNA) is a recently discovered RNA
Found in nucleus of eukaryotes
Small ( nucleotides long)
Forms complexes with protein and form small nuclear ribonucleoprotein particles (snRNPs)
snRNPs help with processing of initial mRNA transcribed from DNA

34. The Structure of the Prokaryotic Ribosome
Figure 9.26 The structure of a typical prokaryotic
ribosome. The individual components
can be mixed, producing functional subunits.
Reassociation of subunits gives rise to an intact
ribosome.