Name: Sean Carlo Suarez

Chem 2065 AY 2023-24

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

DNA and RNA are two kinds of nucleic acids. There are important differences
between DNA and RNA in their secondary and tertiary structures. They differ on
the pentose sugar moiety. Deoxyribose is present in DNA while ribose is present
in RNA in the same position. The difference between ribose and deoxyribose is
that ribose contains a hydroxyl group on the 2’ carbon while deoxyribose doesn’t
have a hydroxyl group on the 2’ carbon.

2. List the levels of structure in nucleic acids.

Just like proteins, nucleic acids have a primary, secondary, and a tertiary
structure. The primary structure of nucleic acids is the order of bases in the
polynucleotide sequence, and the secondary structure is the three-dimensional
conformation of the backbone. The tertiary structure is specifically the
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.

The nucleic acid bases are the nitrogen-containing aromatic compounds that
make up the coding portion of nucleic acids. The nucleic acid bases are of two
types: pyrimidine bases and purine bases. Pyrimidine bases are
nitrogen-containing aromatic compounds that contain a six-membered ring; the
parent compound of several nucleobases such as cytosine, thymine, and uracil.
Purine bases are nitrogen-containing aromatic compounds that contain a
six-membered ring fused to a five-membered ring; the parent compound of the
nucleobases: adenine and guanine.
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.

A nucleoside is a compound that consists of a base and a sugar covalently linked

together. It differs from a nucleotide by lacking a phosphate group in its structure.
In a nucleoside, a base forms a glycosidic linkage with the sugar. The glycosidic
linkage is from the C-1' carbon of the sugar to the N-1 nitrogen of pyrimidines or
to the N-9 nitrogen of purines.
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.

When phosphoric acid is esterified to one of the hydroxyl groups of the sugar
portion of a nucleoside, a nucleotide is formed. A nucleotide is named for the
parent nucleoside, with the suffix -monophosphate added; the position of the
phosphate ester is specified by the number of the carbon atom at the hydroxyl
group to which it is esterified
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)
 Box: 3'-5'-phosphodiester bond

A 3'-5'-phosphodiester bond is formed when phosphoric acid is esterified to the 3'

hydroxyl of one nucleoside and the 5' hydroxyl of another nucleoside. This is the
backbone of nucleic acids.

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 has two polynucleotide chains wrapped around each
other. This double helical structure was based on model building and X-Ray
diffraction patterns. Rosalind Franklin and Maurice WIlkins determined X-Ray
patterns which were added to information from chemical analyses that showed
that the amount of A was always the same as the amount of T, and that the
amount of G always equaled the amount of C. Chargaff’s rule is what it is called.
It was named after the Austrian scientist, Erwin Chargaff who discovered it. Both
of these lines of evidence were used to conclude that DNA consists of two
polynucleotide chains wrapped around each other to form a helix.

Hydrogen bonds between bases on opposite chains determine the alignment of

the helix, with the paired bases lying in planes perpendicular to the helix axis. An
adenine–thymine base pair has two hydrogen bonds between the bases; a
guanine-cytosine base pair has three.

The sugar–phosphate backbone is the outer part of the helix. The chains have
antiparallel directions, one 3' to 5' and the other 5' to 3’. The inside diameter of
the sugar–phosphate backbone of the double helix is about 11 Å (1.1 nm). The
distance between the points of attachment of the bases to the two strands of the
sugar–phosphate backbone is the same for the two base pairs A–T and G–C,
about 11 Å (1.1 nm), which allows for a double helix with a smooth backbone and
no overt bulges. 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. 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. DNA is complexed with histones (Eukaryotic DNA) or associated
with counter ions such as NA+ or Mg+ which is positively charged for it to
neutralize the negative charge of the DNA.

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)

There are different conformations for DNA and these are A-DNA, B-DNA, and
Z-DNA with B-DNA being the most common form and is the conformation being
discussed in the previous numbers.

A-DNA has 11 base pairs in one turn of the helix. Its base pairs are not
perpendicular to the helix axis, but lie at an angle of about 20° to the
perpendicular. A-DNA also is a right-handed helix just like the B-DNA. This
means that it wraps clockwise.
Z-DNA meanwhile, is left-handed, or twists in an anticlockwise direction. Z-DNA
is known to occur in nature, most often when there is a sequence of alternating
purine– pyrimidine, such as CGCGCG. The Z form of DNA can be considered a
derivative of the B form of DNA, produced by flipping one side of the backbone
180° without having to break either the backbone or the hydrogen bonding of the
complementary bases.

B-DNA has been considered the normal, physiological form of DNA.

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

Base stacking is the interactions between bases that are next to each other in a
DNA chain. The ring portions of the DNA bases are very hydrophobic and
interact with each other via hydrophobic bonding (van der Waals interactions) of
their pi-cloud electrons. In standard B-DNA, each base pair is rotated 32° with
respect to the preceding one. Although this is beneficial and allows for the bases
to have maximum pairing, it’s not optimum with stacking, this is called helical
twist. There’s another way of twisting the helix which is known as the propeller
twist. In this form, the base-pairing distances are less optimal, but the base
stacking is more optimal, and 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.

The DNA molecule is not really stiff and it can fold back on itself. The DNA
molecule has a length considerably greater than its diameter. In order for it to fit
inside the cell, more specifically in the organelles: nucleus, mitochondria, and
chloroplast, it needs to fold back on itself.

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.

DNA in prokaryotes are circular, and this DNA forms supercoils. If the strands
are underwound, they form negative supercoils. If they are overwound, they form
positive supercoils. Negative supercoils have fewer than the normal number of
turns of the helix. Positive supercoils have more than the normal number of turns
of the helix.
12. Explain the roles of topoisomerases or gyrases in creating or eliminating
supercoiling in prokaryotic DNA.

Naturally occurring circular DNA is negatively supercoiled except during

replication, when it becomes positively supercoiled. Topoisomerases are the
enzymes that are involved in changing the supercoiled state of the DNA.
Topoisomerases have two classes. Class I topoisomerases cut the
phosphodiester backbone of one strand of DNA, pass the other end through, and
then reseal the backbone. Class II topoisomerases cut both strands of DNA,
pass some of the remaining DNA helix between the cut ends, and then reseal. In
either case, supercoils can be added or removed. Meanwhile, DNA gyrase is a
bacterial topoisomerase that induces negative supercoiling in DNA.

13. Explain how supercoiling occurs in eukaryotic DNA (histones, chromatin,

nucleosome, octamer, spacer regions, nonhistone proteins, linker)

The Nuclear DNA supercoiling of eukaryotes is much more complicated than that
of the circular DNA of prokaryotes. Eukaryotic DNA has many proteins,
especially basic proteins which have abundant positively charged side chains at
physiologically neutral pH. Electrostatic attraction between the negatively
charged phosphate groups on the DNA and the positively charged groups on the
proteins favors the formation of complexes of this sort. This results in chromatin.
Histones are the principal proteins in chromatin, of which there are five main
types, called H1, H2A, H2B, H3, and H4. In the chromatin structure, the DNA is
tightly bound to all types of histone except H1. It is very simple to remove the H1
protein from chromatin, but it is more challenging to separate the other histones
from the complex. There are also other proteins in the DNA of eukaryotes but
they are not as abundant as histones. In electron micrographs, chromatin
resembles beads on a string. Each bead is called a nucleosome.

A histone core is wrapped by DNA. This protein core is called an octamer, which
includes two molecules of each type of histone but H1; the composition of the
octamer is (H2A)2(H2B)2(H3)2(H4)2. The “string” portions are called spacer
regions; they consist of DNA complexed to some H1 histone and nonhistone
proteins. As the DNA coils around the histones in the nucleosome, about 150
 base pairs are in contact with the proteins; the spacer region is about 30 to 50
base pairs long.

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)

Energy must be added to a sample of DNA to break the hydrogen bonds and to
disrupt the stacking interactions. This is usually carried out by heating the DNA in
solution. This heating is also termed “melting”. Heat denaturation is a way to
obtain single-stranded DNA.

As the DNA is heated and the strands separate, the wavelength of absorption
does not change, but the amount of light absorbed increases. This is called
hyperchromicity.

The G-C base pair has three hydrogen bonds, and an A-T base pair has only
two. The higher the percentage of G-C base pairs, the higher the melting
temperature of a DNA molecule. In addition to the effect of the base pairs, G-C
pairs are more hydrophobic than A-T pairs, so they stack better, which also
affects the melting curve.

Renaturation can be obtained through slow cooling. Renaturation is also called

annealing. Once the strands are separated, each one may anneal with its original
partner or with another complementary molecule.

15. Describe the structures and functions of transfer RNA, ribosomal RNA, and
messenger RNA.
 tRNA is small, about 80 nucleotides long. It exhibits extensive intrachain
hydrogen bonding, represented in two dimensions by a cloverleaf structure
(secondary structure) Base pairs substitutes uracil for thymine. and it transports
amino acids to the site of protein synthesis. rRNA varies in size as there are
several kinds but are usually large and are complexed with proteins and its role is
to combine with proteins to form ribosomes, the site of protein synthesis. mRNA
varies in size with the protein and its role is to direct the sequence of amino acids
in 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)

snRNA - processes initial mRNA to its mature form in eukaryotes

miRNA - affects gene expression, important in growth and development
siRNA - affects gene expression, used by scientists to knock out a gene being
studied
lncRNA - affect development and be related to certain disease states