Mamalapat, Mohamidin K 9/17/2023.

Chem 2065 AY2023-24

09 Nucleic Acids: How Structure Conveys Information

1. Define deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

There are two kinds of nucleic acids namely the deoxyribonucleic acid (DNA) and
the ribonucleic acid (RNA). Both of their structures contain a five-carbon sugar, a
backbone, a phosphate group, and a nitrogenous base. However, they also have
differences:

(a) DNA utilizes the sugar deoxyribose while RNA contains the ribose
(b) DNA is double stranded while RNA is single stranded
(c) Bases for DNA are adenine, thymine cytosine, and guanine while in RNA, it uses all
the other three except for thymine but instead uses uracil
(d) DNA is responsible for the code for the activity of the cell while RNA converts the code
into proteins which will carry out cellular functions

2. List the levels of structure in nucleic acids

• Primary structure – order of bases in the nucleotides
• Secondary structure – three-dimensional conformation of the backbone
• Tertiary structure – supercoiling of the molecule

3. Draw the structures of the nucleobases: pyrimidine bases (cytosine, thymine,

and uracil) and the purine bases (adenine and guanosine) Pay attention to the IUPAC
numbering scheme in the nucleobases
4. Draw and name the nucleosides formed from the nucleobases with
either ribose or deoxyribose (For now, do not worry too much about glycosidic bonds
or glycosidic linkages. We will encounter it again when we discuss carbohydrates.) Pay
attention to the numbering scheme in ribose and deoxyribose compared to the numbering
scheme in the nucleobases

5. Draw and name the nucleotides formed from nucleosides with phosphoric acid (Note that
this is a phosphoester bond) Note that monophosphates, diphosphates, or triphosphates
may be formed. Also take note of nucleotides that are exclusive to DNA and nucleotides
that are exclusive to RNA
6. Draw polynucleotides (fragments of RNA or DNA chain) formed from nucleotides. (Note
the formation of a 3'-5'-phosphodiester bond in this process. Pay special attention to
the differences between DNA and RNA)

7. Describe the structure of the DNA double helix (Read on the discoveries of Chargaff,
Franklin and Wilkins. Watson and Crick model ---based on X-ray diffraction data obtained
by Franklin) handedness, complementary strands, antiparallel strands, inside
diameter, outside diameter, specific base-pairing A-T and G-C, major groove and
minor groove, pitch, number of base pairs per pitch, distance between successive
base pairs, charge on the polynucleotide, counter-ions)
 The DNA double helix coiled strands run in antiparallel direction with hydrogen
bonds between the complementary bases. Ten base pairs span a complete turn which
covers a distance of 3.4 nanometers and individual base pairs are 0.34 nanometers apart.
The places where the strands cross hide base pairs that extend perpendicular to the
viewer. The inside diameter is 1.1 nanometers while the outside is 2 nanometers. Two
grooves can be found within the cylindrical outline. The minor groove and the major groove
which are large enough to accommodate the polypeptide chains. Along each strand, many
negatively charged phosphate groups are found.

8. Differentiate between the different DNA conformations ( A-DNA, B-DNA, Z-DNA) B-DNA
is the most prevalent form (DNA:RNA hybrids, significance of sequence and methylation
in Z-DNA)
• A-DNA – has 11 base pairs for each turn of the helix which are not perpendicular
to the helix axis, instead it lies at an angle about 20o to the perpendicular. It also
has a right-handed helix which means that the helix winds upward in the direction
like how the fingers of the right-hand curl when the thumb is pointing upward. A-
DNA was originally found in dehydrated DNA samples and was believed to be an
artifact of DNA preparation. DNA:RNA hybrids can adopt this conformation.
• B-DNA – principal form that occurs in nature and the most common form of the
DNA double helix. It is the nature of the hydrogen bonds between the purines and
pyrimidines. Like A-DNA it is also a right-handed helix.
• Z-DNA – left-handed helix which means that it winds in the direction of the fingers
of the left hand. Z-DNA is also known to occur in nature, often when there is a
sequence of alternating purine and pyrimidine. It can also be considered as a
derivative of the B form of DNA produced by flipping one side of the backbone
180o without breaking either backbone or the hydrogen bonding of the
complementary bases. Z-DNA has a zigzag look of the phosphodiester backbone
when in side view, thus its name.

9. Explain how base stacking and additional twisting further stabilize the DNA double
helix

In base stacking, the hydrophobic ring portions of the DNA bases interact with
each other via hydrophobic bonding (van der Waals interactions) of their pi-cloud
interactions. Even the single-stranded DNA form structures in which the bases can stack.
 Additional twisting gives way to more optimal base stacking. Propeller twist
happens in many bases where the base-pairing distances are less optimal but the base
stacking is more optimal. Water is eliminated from the minor-groove contacts with the
bases.

10. Explain why DNA supercoiling is necessary for DNA to fit inside the cell

DNA molecules has greater length than its diameter thus it is not stiff and is able
to fold back on itself like how proteins fold into their tertiary structures. Extra twists cause
DNA to form supercoils. Lengths of the DNA can be so much greater than the cell thus it
is difficult to package this genetic material into the cell. The supercoiling is necessary to
reduce the space and allows the DNA to fit.

11. Differentiate between positive supercoiling and negative supercoiling (You can
visualize this by taking a twisted rope (or coils or spirals you can find at home) then twist
it either clockwise or counterclockwise. You will notice the helix either becoming tighter
(positive supercoiling) or becoming looser (negative supercoiling). This is inherent in
helices or coils.

• Positive supercoils are circular DNA with more than the normal number of turns of the
helix (overwound) while the negative supercoils is still a circular DNA however it has
fewer turns of the helix compared to the normal (underwound).
 • Negative supercoiling introduces a torsional stress which favors unwinding of the B-
DNA helix, while the positive supercoiling overwinds such a helix. However, both forms
compact the DNA.

12. Explain the roles of topoisomerases or gyrases in creating or eliminating supercoiling

in prokaryotic DNA

Topoisomerases are enzymes that change the supercoiled state of the DNA. It falls
into two classes:

• Class I topoisomerases which cut the phosphodiester backbone of one strand of

the DNA, pass the other end through, and then reseal the backbone.
• Class II cut both strands of the DNA, pass some of the remaining DNA helix
between the cut ends, and then reseal. DNA gyrases is a bacterial topoisomerase
that introduces supercoils into DNA.
13. Explain how supercoiling occurs in eukaryotic DNA (histones, chromatin,
nucleosome, octamer, spacer regions, nonhistone proteins, linker)

• Compared to prokaryotes, supercoiling of the DNA is more complicated. The

eukaryotic DNA is complexed with a number of proteins where most are basic proteins
that have positively charged side chains at neutral pH. The chromatin occurs when
electrostatic attraction between the negatively charged phosphate groups of the DNA
and the positively charged groups on the protein favors the complexes. Histones are
the principal proteins in chromatin.
• Chromatin resembles beads on a string if viewed in an electron micrograph. Each of
the “bead” is a nucleosome that has a DNA wrapped around a histone core. This
protein core is an octamer. The “string” portions are the spacer regions which have
DNA complexed to some H1 histone and nonhistone proteins.

14. Explain how the denaturation of DNA can be followed through spectroscopy ("melting"
of DNA, hyperchromicity, renaturation, effect of base composition on the transition
temperature, annealing or renaturation)
• The melting, or the heat denaturation of the DNA, can be monitored through
observation of the absorption of UV light. The bases absorb light in a 260-nm-
wavelength region. Wavelength does not change as DNA is heated and strands
separate but amount of light absorbed increases which is an effect called
hyperchromicity. Since the bases interact differently in the stacked and unstacked
orientations, there is a change in absorption. There is a midpoint of the melting
curve, or also called the transition temperature. Transition temperature increases
as the G-C content increases. In addition, G-C pairs are more hydrophobic than
AT so they can stack better, which affects the melting curve.
• Renaturation is possible on slow cooling. Separated strands can recombine and
form the same base pairs. Renaturation can also be called annealing. So once the
strands are separated, each one may anneal with its original pair or with another
complementary molecule.
15. Describe the structures and functions of transfer RNA, ribosomal
RNA, and messenger RNA
• Transfer RNA – small, single-stranded polynucleotide chain between 73 to 94
nucleotide residues long; exhibits extensive interchain bonding which is
 represented in two dimensions by a cloverleaf structure; functions to transport
amino acids to the site of protein synthesis
• Ribosomal RNA – molecules tend to be quite large, and only few types exist in
cells; combines with the proteins to form ribosomes which is the site of the protein
synthesis
• Messenger RNA – least abundant and molecule size depends on the size of the
protein; direct amino acid sequence of the proteins

16. Describe the functions of small nuclear RNA, micro RNA, small interfering
RNA, and long noncoding RNA (These are relatively recently discovered so they're not
as extensively studied as the three mentioned in the previous objective)

• Small nuclear RNA (snRNA) – processing of pre-messenger RNA in the nucleus

• Micro RNA (miRNA) – found to be part of one of the oldest evolutionary relationships
between bacteria and bacteriophages; RNA silencing and post-transcriptional
regulation of gene expression
• Small interfering RNA (siRNA) – main players in RNA interference; protect cell from
exogenous mRNA attacks; degrades growing mRNA and stops gene expression
• Long noncoding RNA (lncRNA) – regulates epigenetic modification primarily in the
nucleus, regulating gene transcription