DNA Rep and RNA structure well explained

DNA Structure
 Watson and Crick proposed that DNA is made up of two strands
that are twisted around each other to form a right-handed helix.
The two DNA strands are antiparallel, such that the 3ʹ end of one
strand faces the 5ʹ end of the other.
 Eg. 5’ CAGCAGCAG 3’ / 5’ CTGCTGCTG 3’.
The 3ʹ end of each strand has a free hydroxyl group, while the 5ʹ end
of each strand has a free phosphate group.

DNA Structure
 The sugar and phosphate of the polymerized nucleotides form the
backbone of the structure, whereas the nitrogenous bases are stacked
inside.
 These nitrogenous bases on the interior of the molecule interact with
each other, base pairing.
The asymmetrical spacing of the sugar-phosphate backbones
generates major grooves (where the backbone is far apart) and minor
grooves (where the backbone is close together).

DNA Structure
 These grooves are locations where proteins can bind
to DNA. The binding of these proteins can alter the
structure of DNA, regulate replication, or regulate
transcription of DNA into RNA.

(a) The sugar-phosphate backbones are on the outside of the double helix and purines and pyrimidines form the “rungs” of the DNA
helix ladder.
(b) The two DNA strands are antiparallel to each other.
(c) The direction of each strand is identified by numbering the carbons (1 through 5) in each sugar molecule.
The 5ʹ end is the one where carbon #5 is not bound to another nucleotide; the 3ʹ end is the one where carbon #3 is not bound to another
nucleotide.

BASE PARING
 Base pairing takes place between a purine and pyrimidine.
 In DNA, adenine (A) and thymine (T) are complementary base
pairs, and cytosine (C) and guanine (G) are also complementary base
pairs, explaining Chargaff’s rules (Figure 7).
 The base pairs are stabilized by hydrogen bonds; adenine and
thymine form two hydrogen bonds between them, whereas cytosine
and guanine form three hydrogen bonds between them.

Hydrogen bonds form between complementary nitrogenous bases on the interior of DNA.

LABOURATORY SEPARATION
 In the laboratory, exposing the two DNA strands of the double helix
to high temperatures or to certain chemicals can break the hydrogen
bonds between complementary bases, thus separating the strands into
two separate single strands of DNA (single-stranded DNA [ssDNA]).
This process is called DNA denaturation and is analogous to protein
denaturation.

LABOURATORY SEPARATION
 The ssDNA strands can also be put back together as double-stranded DNA
(dsDNA), through reannealing or renaturing by cooling or removing the
chemical denaturants, allowing these hydrogen bonds to reform.
 The ability to artificially manipulate DNA in this way is the basis for
several important techniques in biotechnology (Figure 8).
 Because of the additional hydrogen bonding between the C = G base pair,
DNA with a high GC content is more difficult to denature than DNA with a
lower GC content.

In the lab, the double helix can be denatured to single-stranded DNA through exposure to heat
or chemicals, and then renatured through cooling or removal of chemical denaturants to allow
the DNA strands to reanneal.

DNA Nucleotides
 The building blocks of nucleic acids are nucleotides. Nucleotides that compose
DNA are called deoxyribonucleotides.
 The three components of a deoxyribonucleotide are a five-carbon sugar called
deoxyribose, a phosphate group, and a nitrogenous base, a nitrogen-containing
ring structure that is responsible for complementary base pairing between
nucleic acid strands (Figure 1).
 The carbon atoms of the five-carbon deoxyribose are numbered 1ʹ, 2ʹ, 3ʹ, 4ʹ, and
5ʹ (1ʹ is read as “one prime”).
 A nucleoside comprises the five-carbon sugar and nitrogenous base.

DNA Nucleotides
 Nitrogenous bases within DNA are categorized into the two-ringed purines
adenine and guanine and the single-ringed pyrimidines cytosine and thymine.
Individual nucleoside triphosphates combine with each other by covalent bonds
known as 5ʹ-3ʹ phosphodiester bonds, or linkages whereby the phosphate group
attached to the 5ʹ carbon of the sugar of one nucleotide bonds to the hydroxyl
group of the 3ʹ carbon of the sugar of the next nucleotide.
Phosphodiester bonding between nucleotides forms the sugar-phosphate
backbone

(a) Each deoxyribonucleotide is made up of a sugar called deoxyribose, a phosphate group, and
a nitrogenous base—in this case, adenine.
(b) The five carbons within deoxyribose are designated as 1ʹ, 2ʹ, 3ʹ, 4ʹ, and 5ʹ.

Nitrogenous bases within DNA are categorized into the two-ringed purines adenine and
guanine and the single-ringed pyrimidines cytosine and thymine. Thymine is unique to DNA.

Phosphodiester bonds form between the phosphate group attached to the 5ʹ carbon of one
nucleotide and the hydroxyl group of the 3ʹ carbon in the next nucleotide, bringing about
polymerization of nucleotides in to nucleic acid strands. Note the 5ʹ and 3ʹ ends of this nucleic
acid strand.

DNA Function
 DNA stores the information needed to build and control the cell.
The transmission of this information from mother to daughter cells is called
vertical gene transfer and it occurs through the process of DNA
replication.
 DNA is replicated when a cell makes a duplicate copy of its DNA, then the
cell divides, resulting in the correct distribution of one DNA copy to each
resulting cell.
DNA can also be enzymatically degraded and used as a source of
nucleosides and nucleotides for the cell.
Unlike other macromolecules, DNA does not serve a structural role in cells.

RNA STRUCTURE
 RNA or ribonucleic acid is a polymer of nucleotides which is made up of a
ribose sugar, a phosphate, and bases such as adenine, guanine, cytosine, and
uracil.
RNA has a structure very similar to that of DNA.
 The key difference in RNA structure is that the ribose sugar in RNA has a
hydroxyl (-OH) group which is absent in DNA.
RNA plays a very crucial role in the gene expression pathway by which
genetic information in DNA is coded into proteins that determine cell
function.

RNA (Ribonucleic acid )
 RNA is a polymer of
ribonucleotides linked
together by 3’-5’
phosphodiester linkage

Types of RNA
 In both prokaryotes and eukaryotes, there are three main types of
RNA – messenger RNA or mRNA, ribosomal or rRNA, and transfer
RNA or tRNA. These 3 types of RNA are discussed below.
Other RNA include: small nuclear RNA (SnRNA),
 micro RNA(miRNA) and
 small interfering RNA(Si RNA) and
 heterogeneous nuclear RNA (hnRNA).

Messenger RNA (mRNA)
 mRNA accounts for just 5% of the total RNA in the cell.
 mRNA is the most heterogeneous of the 3 types of RNA in terms of both
base sequence and size.
 It carries the genetic code copied from the DNA during transcription in the
form of triplets of nucleotides called codons.
Each codon specifies a particular amino acid, but one amino acid can be
coded by many different codons.
Although there are 64 possible codons or triplet bases in the genetic code,
only 20 of them represent amino acids; there are also 3 stop codons.

Messenger RNA (mRNA)
 As part of post-transcriptional processing in eukaryotes, the 5’ end of
mRNA is capped with a guanosine triphosphate nucleotide, which
helps in mRNA recognition during translation or protein synthesis.
Similarly, the 3’ end of an mRNA has a poly A tail or multiple
adenylate residues added to it, which prevent enzymatic degradation of
mRNA. Both 5’ and 3’ end of an mRNA imparts stability to the
mRNA.

Ribosomal RNA (rRNA)
 rRNAs are found in the ribosomes and account for 80% of the total
RNA present in the cell.
 Ribosomes are composed of a large subunit called the 50S and a
small subunit called the 30S, each of which has its own rRNA
molecules.
Different rRNAs present in the ribosomes include small rRNAs and
large rRNAs, which denote their presence in the small and large
subunits of the ribosome.

Ribosomal RNA (rRNA)
 rRNAs combine with proteins in the cytoplasm to form ribosomes,
which act as the site of protein synthesis and has the enzymes needed
for the process.
 These complex structures travel along the mRNA molecule during
translation and facilitate the assembly of amino acids to form a
polypeptide chain.
 They bind to tRNAs and other molecules that are crucial for protein
synthesis.
 In bacteria, the small and large rRNAs contain about 1500 and 3000
nucleotides, respectively, whereas in humans, they have about 1800
and 5000 nucleotides, respectively.
However, the structure and function of ribosomes is largely similar
across all species.

Transfer RNA (tRNA)
 tRNA is the smallest of the 3 types of RNA having about 75-95 nucleotides.
 tRNAs are an essential component of translation, where their main function is the
transfer of amino acids during protein synthesis.
 Therefore they are called transfer RNAs.
 Each of the 20 amino acids has a specific tRNA that binds with it and transfers it
to the growing polypeptide chain.
tRNAs also act as adapters in the translation of the genetic sequence of mRNA
into proteins.
 Therefore they are also called adapter molecules.

Transfer RNA (tRNA)
 tRNAs have a clover leaf structure which is stabilized by
strong hydrogen bonds between the nucleotides.
 Apart from the usual 4 bases, they normally contain some
unusual bases mostly formed by methylation of the usual
bases, for example, methyl guanine and methylcytosine.

Small RNA
 Most of these molecules are complexed with proteins to
form ribonucleoproteins and are distributed in the nucleus, in
the cytoplasm, or in both.
 They range in size from 20 to 300 nucleotides and are
present in 100,000 – 1,000,000 copies per cell.

Small Nuclear RNAs (snRNAs)
1. Small Nuclear RNAs (snRNAs)
 snRNAs, a subset of the small RNAs, are significantly involved in mRNA
processing and gene regulation.
2. Micro RNAs, miRNAs, and Small Interfering RNAs, siRNAs
 These two classes of RNAs represent a subset of small RNAs; both play
important roles in gene regulation.
 miRNAs and siRNAs cause inhibition of gene expression by decreasing
specific protein production albeit apparently via distinct mechanisms

Significance of mi RNAs and siRNAs
 Both miRNAs and siRNAs represent exciting new
potential targets for therapeutic drug development in
humans.
 In addition, siRNAs are frequently used to decrease or
"knock-down" specific protein levels in experimental
procedures in the laboratory, an extremely useful and
powerful alternative to gene-knockout technology.

Differences between RNA and DNA
S.No. RNA DNA
1 Single stranded mainly except
when self-complementary
sequences are there it forms a
double stranded structure (Hair
pin structure)
Double stranded (Except for certain viral DNA s
which are single stranded)
2 Ribose is the main sugar The sugar moiety is deoxyribose
3 Pyrimidine components differ.
Thymine is never found(Except tRNA)
Thymine is always there but uracil is never found
4 Being single stranded structure-
It does not follow Chargaff’s rule
It does follow Chargaff's rule. The total purine
content in a double stranded DNA is always equal
to pyrimidine content.
5 RNA can be easily destroyed by alkalies to
cyclic diesters of mono nucleotides.
DNA resists alkali action due to
the absence of OH group at 2’ position
6 RNA is a relatively a labile
molecule, undergoes easy and
spontaneous degradation
DNA is a stable molecule. The spontaneous
degradation is very 2 slow. The genetic information
can be stored for years together without any
change.

Differences between RNA and DNA
S.No. RNA DNA
7 Mainly cytoplasmic, but also present in nucleus (primary
transcript and small nuclear
RNA)
Mainly found in nucleus, extra nuclear DNA is found in
mitochondria, and plasmids etc
8 The base content varies from
100- 5000. The size is variable.
Millions of base pairs are there
depending upon the organism
9 There are various types of RNA –
mRNA, r RNA, t RNA, Sn RNA, Si
RNA, mi RNA and hn RNA. These
RNAs perform different and specific functions.
DNA is always of one type and performs the function of storage
and transfer of genetic information.
10 No variable physiological forms
of RNA are found. The different
types of RNA do not change
their forms
There are variable forms of
DNA (A to E and Z)
11 RNA is synthesized from DNA, it cannot form DNA (except
by the action of reverse transcriptase).
It cannot duplicate (except in
certain viruses where it is a genomic material)
DNA can form DNA by replication, it can also form RNA by
transcription.
12 Many copies of RNA are present
per cell
Single copy of DNA is present per cell.

DNA Rep and RNA structure well explained

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