DNA AND RNA WORLD

Ribonucleic

acid (RNA)

implicated

in

is

a polymeric molecule

various

biological

roles

in coding, decoding, regulation,

and expression of genes.

RNA

acids,

and DNA arenucleic

with proteins and carbohydrates,

and,

constitute

the

along
three

major macromolecules essential for all known forms of life.

Like DNA, RNA is assembled as a chain of nucleotides, but
unlike DNA it is more often found in nature as a singlestrand folded onto itself, rather than a paired doublestrand. Cellular organisms use messenger RNA (mRNA) to
convey genetic information (using the letters G, U, A, and
C

to

denote

the

nitrogenous

bases guanine, uracil, adenine, andcytosine) that directs

synthesis of specific proteins. Many viruses encode their
genetic information using an RNA genome.
Some RNA molecules play an active role within cells by
catalyzing

biological

reactions,

controlling gene

expression, or sensing and communicating responses to

cellular signals. One of these active processes is protein
synthesis, a universal function wherein mRNA molecules
direct the assembly of proteins on ribosomes. This process
uses transfer

RNA (tRNA)

molecules

to

deliver amino

acids to the ribosome, where ribosomal RNA (rRNA) then

links amino acids together to form proteins.
1

Comparison with DNA

BASES IN AN RNA MOLECULE.

Three-dimensional representation of the 50S ribosomal

subunit. Ribosomal RNA is in ochre, proteins in blue. The
active site is a small segment of rRNA, indicated in red.
The chemical structure of RNA is very similar to that
ofDNA, but differs in three main ways:

Unlike double-stranded DNA, RNA is a single-stranded

molecule[1] in many of its biological roles and has a
2

much shorter chain of nucleotides. [2]However, RNA can,

by

complementary

base

pairing,

form

intrastrand

double helixes, as in tRNA.

While

DNA

contains deoxyribose,

RNA

containsribose[3] (in deoxyribose there is no hydroxyl

group attached to the pentose ring in the 2' position).
These hydroxyl groups make RNA less stable than DNA
because it is more prone to hydrolysis.

The

complementary

base

to adenine in

DNA

isthymine, whereas in RNA, it is uracil, which is

anunmethylated form of thymine.[4]
Like

DNA,

most

biologically

including mRNA, tRNA, rRNA, snRNAs,

active
and

RNAs,
othernon-

coding RNAs, contain self-complementary sequences that

allow parts of the RNA to fold [5]and pair with itself to form
double helices. Analysis of these RNAs has revealed that
they are highly structured. Unlike DNA, their structures do
not consist of long double helices, but rather collections of
short helices packed together into structures akin to
proteins.

In

this

chemical catalysis,

fashion,
like

RNAs

can

enzymes.[6] For

achieve
instance,

determination of the structure of the ribosomean

enzyme that catalyzes peptide bond formationrevealed
that its active site is composed entirely of RNA. [7]

STRUCTURED

Watson-Crick base pairs in a siRNA(hydrogen atoms are

not shown)
Each nucleotide in

RNA

contains

a ribose sugar,

with

carbons numbered 1' through 5'. A base is attached to the

1'

position,

in

general, adenine (A), cytosine(C), guanine (G),

or uracil (U). Adenine and guanine are purines, cytosine
and uracil are pyrimidines. A phosphate group is attached
to the 3' position of one ribose and the 5' position of the
next. The phosphate groups have a negative charge each
at physiological pH, making RNA a charged molecule
(polyanion). The bases form hydrogen bonds between
cytosine and guanine, between adenine and uracil and
between guanine and uracil. [8] However, other interactions
are possible, such as a group of adenine bases binding to
each other in a bulge,[9] or the GNRA tetraloop that has a
guanineadenine base-pair.[8]

CHEMICAL STRUCTURE OF RNA

An important structural feature of RNA that distinguishes it
from DNA is the presence of a hydroxyl group at the 2'
position of the ribose sugar. The presence of this
functional group causes the helix to mostly adopt the Aform geometry,[10] although in single strand dinucleotide
contexts, RNA can rarely also adopt the B-form most
commonly observed in DNA.[11] The A-form geometry
results in a very deep and narrow major groove and a
shallow and wide minor groove. [12] A second consequence
of the presence of the 2'-hydroxyl group is that in
conformationally flexible regions of an RNA molecule (that
is, not involved in formation of a double helix), it can
chemically attack the adjacent phosphodiester bond to
cleave the backbone.[13]

SECONDARY STRUCTURE OF A TELOMERASE RNA.

RNA is transcribed with only four bases (adenine, cytosine,
guanine and uracil),[14]but these bases and attached
sugars can be modified in numerous ways as the RNAs
mature. Pseudouridine (), in which the linkage between
uracil and ribose is changed from a CN bond to a CC
bond, and ribothymidine (T) are found in various places
(the most notable ones being in the TC loop of tRNA).
[15]

Another notable modified base is hypoxanthine, a

deaminated

adenine

base

whose nucleoside is

called inosine (I). Inosine plays a key role in the wobble

hypothesis of the genetic code.[16]
There are more than 100 other naturally occurring
modified nucleosides,[17] The greatest structural diversity
of

modifications

pseudouridine

can

be

and

found

in tRNA,[18] while

nucleosides

with 2'-O-

methylribose often present in rRNA are the most common.

[19]

The specific roles of many of these modifications in

RNA are not fully understood. However, it is notable that,

in

ribosomal

RNA,

many

of

the

post-transcriptional

modifications occur in highly functional regions, such as

the peptidyl transferase center and the subunit interface,
implying that they are important for normal function. [20]
The functional form of single-stranded RNA molecules, just
like

proteins,

frequently

requires

specific tertiary

structure. The scaffold for this structure is provided

by secondary structural elements that are hydrogen bonds
6

within the molecule. This leads to several recognizable

"domains"

of

secondary

structure

like hairpin

loops,

bulges, and internal loops.[21] Since RNA is charged, metal

ions such as Mg2+ are needed to stabilise many secondary
and tertiary structures.[22]
The

naturally

occurring enantiomer of

RNA

is D-RNA

composed of D-ribonucleotides. All chirality centers are

located in theD-ribose. By the use of L-ribose or rather Lribonucleotides, L-RNA can be synthesized. L-RNA is much
more stable against degradation by RNase.
Like other structured biopolymers such as proteins, one
can define topology of a folded RNA molecule. This is often
done based on arrangement of intra-chain contacts within
a folded RNA, termed as circuit topology.
SYNTHESIS
Synthesis of RNA is usually catalyzed by an enzymeRNA
polymeraseusing DNA as a template, a process known
astranscription. Initiation of transcription begins with the
binding of the enzyme to a promoter sequence in the DNA
(usually found "upstream" of a gene). The DNA double
helix is unwound by the helicase activity of the enzyme.
The enzyme then progresses along the template strand in
the 3 to 5 direction, synthesizing a complementary RNA
molecule with elongation occurring in the 5 to 3
direction.

The

DNA

sequence

also

termination of RNA synthesis will occur.

7

dictates

where

Primary transcript RNAs are often modified by enzymes

after transcription. For example, a poly(A) tail and a 5'
cap are

added

to

eukaryotic pre-mRNA and introns are

removed by the spliceosome.

There

are

also

number

of RNA-dependent

RNA

polymerases that use RNA as their template for synthesis

of a new strand of RNA. For instance, a number of RNA
viruses (such as poliovirus) use this type of enzyme to
replicate
Deoxyribonucleic acid
In the middle of the 1900s biologists were wondering
how genes work. What they are made of, and how
they determine the characteristics of organism
If the structures that carry genetic information could
be identified, it might be possible to understand how
genes control the inherited characteristics of living
things
How does DNA do the following things?
1. Carry info from one generation to the next
2. Put info to work by determining the inheritable
characteristics
3. Copies itself, every time a cell divides
Nucleotides
Units that make up DNA molecule
Made of three parts
8

1. 5 carbon sugar (deoxyribose)

2. Phosphate group
3. Nitrogen bases
4 kinds of nitrogen bases
1. Adenine

(A)

2. Guanine (G)
3. Cytosine (C)
4. Thymine (T)
X-Ray Evidence
There were 2 strands
Strands were twisted around each other (helix)
The nitrogen bases are in the middle
The Double Helix
Francis Crick & James Watson
Trying to understand the structure of DNA by building
models
Unsuccessful until early 1953, Watson was shown a
copy of Franklins X-ray pattern
The instant I saw the picture my mouth fell open
and my pulse began to race.
James Watson
Within weeks Watson and Crick had figured out the
structure of DNA
9

 Published their results in a historic one page paper in

April of 1953
Watson and Crick later discovered what held the two
strands together
Hydrogen bonds could form between certain nitrogen
bases and provide enough force to hold the two
strands together
Hydrogen bonds could only form between certain
base pairs adenine and thymine and guanine and
cytosine
This principal is called Base pairing

This explains Chargaffs Rule

Histones
Proteins that coil up DNA
DNA + histone molecules form a bead-like structure
called a nucleosome
Nucleosomes pack together to form thick fibers that
loop and coil together to form chromosomes
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DNA Replication
When Watson and Crick discovered the double helix
structure of DNA they recognized immediately how
DNA could copy itself
The strands are complementary
If you could separate the two strands, the rules of
base pairing would allow you to reconstruct the base
sequence of the other strand
Replication
When the DNA splits into 2 strands, then produces 2
new strands following the rules of base pairing
How Replication Occurs
Replication is carried out by enzymes
Before DNA replicates, the double helix must unwind
and unzip
There

are

many

regulatory

replication
DNA polymerase
11

molecules

used

in

 Joins

individual

nucleotides

to

produce

DNA

molecule, which is a polymer

Also proof reads each new DNA strand
The Steps of Replication
1. DNA unwinds
2. DNA unzips
3. The bases attach from a supply in the cytoplasm
4. Sugar and phosphate groups form the side of each
new strand
Genes
Coded DNA instructions that control the production of
proteins
DNA never leaves the nucleus, therefore the code
must be copied into
RNA, or ribonucleic acid
There are 3 main differences between RNA and DNA
1. It has the sugar ribose, instead of deoxyribose
2. RNA is single stranded
3. RNA contains uracil in place of thymine
RNA is like a disposable copy of a segment of DNA
RNA is like a working copy of a single gene
Types of RNA
1. Messanger RNA (mRNA)
12

 Serve as messangers from DNA to the rest of the cell

2. Ribosomal RNA (rRNA)
Type of RNA that makes up parts of ribosomes
3. Transfer RNA (tRNA)
Transfers each amino acid to the ribosome as it is
specified by the mRNA
Types of RNA
Transcription
RNA molecules are produced by copying part of the
DNA sequence into RNA
Transcription requires an enzyme known as RNA
polymerase
During transcription, RNA polymerase binds to DNA
and separates the DNA strands. RNA polymerase
then uses one strand of DNA as a template from
which nucleotides are assembled into a strand of
RNA.
Q: How does RNA polymerase know where to
start and stop making a RNA copy of DNA?
A: promoters
Signals in DNA that indicate to the enzyme where to
bind to make RNA
Similar signals in DNA cause transcription to stop
RNA Editing
Remember, a lot of DNA doesnt code for proteins
13

 Introns not involved in coding for proteins

Exons code for proteins
The introns get cut out of the RNA molecules before
the final mRNA is made
The Genetic Code
Proteins are made by joining amino acids into long
chains called polypeptides
Each polypeptide contains a combination of any or all
of the 20 different amino acids
The properties of proteins are determined by the
order in which different amino acids are joined
together
The language of mRNA instructions is called the
genetic code
The code is read three letters at a time
Each 3 letter word is called a codon
Each codon corresponds to an amino acid that can be
added to the polypeptide

14

Translation
The sequence of nucleotide bases in an mRNA
molecule serves as instructions for the order in which
amino acids are joined to make a protein
Proteins are put together on ribosomes
Translation
Decoding mRNA into a protein
Steps of Translation
1. mRNA is transcribed from DNA in the nucleus and
released into the cytoplasm
2. mRNA attaches to a ribosome
3.

as each codon of the mRNA molecule moves through

the ribosome, the proper amino acid is transferred to the

growing amino acid chain by tRNA
tRNA carries only one kind of amino acid and three
unpaired bases called the anticodon
4. The amino acid chain continues to grow until the
ribosome reaches a stop codon on the mRNA molecule
The Roles of RNA and DNA
You can compare the different roles played by DNA
and RNA molecules in directing protein synthesis to
the two types of plans used by builders. A master
plan has all the information needed to construct a
building. But builders never bring the valuable
master plan to the building site, where it might be
15

damaged or lost. Instead, they prepare inexpensive,

disposable

copies

of

the

master

plan

called

blueprints. The master plan is safely stored in an

office, and the blueprints are taken to the job site.
Similarly, the cell uses the vital DNA master plan to
prepare RNA blueprints. The DNA molecule remains
in the safety of the nucleus, while RNA molecules go
to the protein-building sites in the cytoplasmthe
ribosomes
Point mutations
Changes in one or a few nucleotides
Ex.) substitutions, insertions, deletions
Frameshift mutations
Mutation that shifts the reading frame of the
genetic message by inserting or deleting a nucleotide
Chromosomal Mutations
Significance of Mutations
Most mutations dont do anything
Mutations that cause drastic changes in proteins
produce

defective

proteins

that

disrupt

normal

biological activities
Mutations are also a source of genetic variability
which can be beneficial
Polyploidy

16

 When plants produce triploid (3N) or tetraploid (4N)

organisms

These plants are often larger and stronger

17