Module 9: Nucleic Acid Biophysics

1. Illustrate the way you understand the RNA/DNA structure. (you can draw and then label). What
is the difference between RNA and DNA?

DNA has a regular structure. It's orientation, width, width between nucleotides, length and
number of nucleotides per helical turn is constant. All of these features were described by Watson
and Crick. Adenine is always opposite thymine, and cytosine is always opposite guanine. The two
strands are held together by hydrogen bonds: two bonds between adenine and thymine and three
bonds between guanine and cytosine. DNA is a string of deoxyribonucleotides. These consist of
three different components. These are the deoxyribose sugar, a phosphate group, and a nitrogen
base. Variation in the nitrogen base composition distinguishes each of the four
deoxyribonucleotides. The basic building block is the deoxyribose sugar. This sugar is
distinguished because it contains a hydrogen (H) atom at the number 2' carbon. Normal ribose has
a hydorxyl (-OH) group at this position. Attached to the 5' carbon is a triphosphate group. This
group is important because in a DNA chain it undergoes a reaction with the 3' OH group to
produce polydeoxynucleotide.
RNA typically is a single-stranded biopolymer. However, the presence of self-
complementary sequences in the RNA strand leads to intrachain base-pairing and folding of the
ribonucleotide chain into complex structural forms consisting of bulges and helices. The three-
dimensional structure of RNA is critical to its stability and function, allowing the ribose sugar
and the nitrogenous bases to be modified in numerous different ways by cellular enzymes that
attach chemical groups (e.g., methyl groups) to the chain. Such modifications enable the
formation of chemical bonds between distant regions in the RNA strand, leading to complex
contortions in the RNA chain, which further stabilizes the RNA structure. Molecules with weak
structural modifications and stabilization may be readily destroyed. As an example, in an initiator
 transfer RNA (tRNA) molecule that lacks a methyl group (tRNAiMet), modification at position 58
of the tRNA chain renders the molecule unstable and hence nonfunctional; the nonfunctional
chain is destroyed by cellular tRNA quality control mechanisms.
The DNA is a double-stranded biomolecule made up of two polynucleotide chains while the
RNA is a single-stranded biomolecule made up of a single polynucleotide chain. Scientists
believe that the DNA is more susceptible to damage- it is the genetic material in almost all living
entity. Thus if one of the strands is damaged, a second strand can be used to repair it or form
another complementary strand like it.
The length of the DNA is much longer in comparison to the RNA. A genome of us contains
coding and non-coding both types of DNA- arranged on chromosomes. If we stretch all the DNA
of a cell it is actually 3 meters long. Hence it is very important to fit it inside the cell. DNA
packaging allows to arrange it on chromosomes and fit inside the cell. Contrary to this, the RNA
is a final functional product transcribed from a DNA therefore it is much shorter than the DNA
(Other non-coding sequences are removed). Interestingly, some double-stranded RNAs are also
found in eukaryotes as well- called microRNA or siRNA. Functionally, the microRNA can’t
form protein, instead, it helps in regulating gene expression through RNA interference
mechanism. The dsRNA is present in very low quantity.
Although both nucleic acids are almost similar, the DNA is made up of the deoxyribose sugar
while the RNA is made up of the ribose sugar only. The deoxyribose sugar lacks one oxygen
molecule and carries hydrogen atom instead of a hydroxyl group at carbon 2. As contrast, the
ribose is a simple sugar which has an oxygen molecule with an additional hydroxyl group at
carbon 2. During the catalytic reaction, the difference of one oxygen makes easy for enzymes to
distinguish DNA from RNA. The DNA is made up of adenine, guanine, cytosine and thymine
while the RNA is made up of the adenine, guanine, cytosine and uracil.

2. What is DNA melting? There is an aspect of DNA melting worth looking into. Why does
unwinding of additional bases or base pairs typically continue in a zipper-like fashion, from
where unwinding began? Why not simply unwind single bases here and there throughout the
molecule? Make a research on the given questions.
DNA melting is the process by which the two complementary strands of a DNA molecule
dissociate into two single strands DNA melting can be achieved by a series of methods such as
heating, adding denaturant to the solvent or mechanically pulling the two ends. At low
temperatures the strands are partially unbound by forming fluctuating loops where the two strands
are locally separated. As the melting temperature is approached the average loops size increases,
yielding full denaturation at TM. Melting of DNA has been extensively studied over the years
both theoretically and experimentally. The natural order-parameter of the denaturation transition
is the fraction of bound base-pairs. This was measured using specific-heat and UV absorption
experiments.
There are four possible bases, A, C, T and G. The bases of one strand pair up with the
bases of the other strand in a very simple way called the base-pairing rule. C pairs up with G and
A pairs up with T. What this means is that the DNA sequence of one strand completely defines
the DNA sequence of the other strand. Because of how the bases pair up, the two strands come
together like a molecular zipper. During replication, the strands are unzipped and each is copied
following the base-pairing rule. So if there is an A, when you make the copy, you should put in a
T and vice versa. The same holds true for G and C. When replication is complete, each new DNA
contains one old and one new strand or one parental and one daughter strand. Every step of DNA
replication needs special molecules to do the work. These molecules are called enzymes. As we
go through this, remember, all that is happening is the DNA is being unzipped and each side of
the zipper is being copied. The first step in DNA replication is to separate or unzip the two
strands of the double helix. The enzyme in charge of this is called a helicase (because it unwinds
the helix). The point where the double helix is opened up and the DNA is copied is called a
replication fork. Once the strands are separated, an enzyme called DNA polymerase copies each
strand using the base-pairing rule. The two strands are not exactly copied the same way. Because
a polymerase can only work along the strand in one direction (5' to 3'), it uses a slightly different
strategy to copy the DNA on each strand: the leading and lagging strand. DNA polymerases are
not doing all this on their own. Many more enzymes help out. For example, there are some
enzymes that stitch up the newly made strands. Some enzymes prime the DNA so that the
polymerases can start copying; other enzymes remove those priming sites and replace them with
proper DNA. The 5' phosphate on each incoming nucleotide is joined by the DNA polymerase to
the 3' OH on the end of the growing nucleic acid chain. As we already noted, the new DNA
strands are synthesized by the addition of DNA nucleotides to the end of an RNA primer. The
new DNA molecule thus has a short piece of RNA at the beginning. DNA polymerases can only
extend a strand in the 5' to 3' direction. The 5' to 3' growth of both new strands means that one of
the strands is made in pieces.

https://genetics.thetech.org/ask/ask24#:~:text=DNA%20is%20made%20of%20two,a
%20part%20of%20the%20nucleotides.&text=Because%20of%20how%20the
%20bases,together%20like%20a%20molecular%20zipper.
https://bio.libretexts.org/Bookshelves/Biochemistry/Book
%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/05%3A_Flow_of_Genetic
_Information/5.01%3A_DNA_Replication