Biochemistry for Medics

http://www.namrata.co/
Biochemistry For Medics 1
RNA (Ribonucleic acid )

RNA is a
polymer of
ribonucleotides
linked together
by 3’-5’
phosphodiester
linkage

Biochemistry For Medics 2

RNA V/S DNA

Biochemistry For Medics 3

Differences between RNA and DNA
S.No. RNA DNA

1) Single stranded mainly except Double stranded (Except for

when self complementary certain viral DNA s which are
sequences are there it forms a single stranded)
double stranded structure (Hair
pin structure)
2) Ribose is the main sugar The sugar moiety is deoxy
ribose
3) Pyrimidine components differ. Thymine is always there but
Thymine is never found(Except uracil is never found
tRNA)
4) Being single stranded structure- It does follow Chargaff's rule.
It does not follow Chargaff’s rule The total purine content in a
double stranded DNA is always
equal to pyrimidine content.

Biochemistry For Medics 4

Differences between RNA and DNA
S.No. RNA DNA
5) RNA can be easily destroyed by DNA resists alkali action due to
alkalies to cyclic diesters of the absence of OH group at 2’
mono nucleotides. position
6) RNA is a relatively a labile DNA is a stable molecule. The
molecule, undergoes easy and spontaneous degradation is
spontaneous degradation very 2 slow. The genetic
information can be stored for
years together without any
change.
7) Mainly cytoplasmic, but also Mainly found in nucleus, extra
present in nucleus (primary nuclear DNA is found in
transcript and small nuclear mitochondria, and plasmids
RNA) etc
8) The base content varies from Millions of base pairs are there
100- 5000. The size is variable. depending upon the organism

Biochemistry For Medics 5

Differences between RNA and DNA
S.No. RNA DNA
9) There are various types of RNA – DNA is always of one type and
mRNA, r RNA, t RNA, Sn RNA, Si performs the function of
RNA, mi RNA and hn RNA. These storage and transfer of genetic
RNAs perform different and information.
specific functions.
10) No variable physiological forms There are variable forms of
of RNA are found. The different DNA (A to E and Z)
types of RNA do not change
their forms
11) RNA is synthesized from DNA, it DNA can form DNA by
can not form DNA(except by the replication, it can also form
action of reverse transcriptase). RNA by transcription.
It can not duplicate (except in
certain viruses where it is a
genomic material )
12) Many copies of RNA are present Single copy of DNA is present
per cell per cell.
Biochemistry For Medics 6
Types of RNA
In all prokaryotic and eukaryotic
organisms, three main classes of RNA
molecules exist-
1) Messenger RNA(m RNA)
2) Transfer RNA (t RNA)
3) Ribosomal RNA (r RNA)
The other are –
o small nuclear RNA (SnRNA),
o micro RNA(mi RNA) and
o small interfering RNA(Si RNA) and
o heterogeneous nuclear RNA (hnRNA).

Biochemistry For Medics 7

Messenger RNA (m-RNA)

Comprises only 5% of the RNA in the cell

Most heterogeneous in size and base sequence
All members of the class function as
messengers carrying the information in a gene to
the protein synthesizing machinery
Biochemistry For Medics 8
Structural Characteristics of
m-RNA
The 5’ terminal end is capped by 7-
methyl guanosine triphosphate cap.
The cap is involved in the
recognition of mRNA by the
translating machinery
It stabilizes m RNA by protecting it
from 5’ exonuclease

Biochemistry For Medics 9

Structural Characteristics of
m-RNA(contd.)
 The 3’end of most m-RNAs have a polymer of
Adenylate residues( 20-250)
 The tail prevents the attack by 3’ exonucleases
Histones and interferons do not contain poly A
tails
 On both 5’ and 3’ end there are non coding
sequences which are not translated (NCS)
The intervening region between non coding
sequences present between 5’ and 3’ end is
called coding region. This region encodes for the
synthesis of a protein.

Biochemistry For Medics 10

Structural Characteristics of
m-RNA

5’ cap and 3’ tail impart stability to m RNA by protecting from

specific exo nucleases.
Biochemistry For Medics 11
Structural Characteristics of
m-RNA(Contd.)
The m- RNA molecules are formed with the help of
DNA template during the process of transcription.
The sequence of nucleotides in m RNA is
complementary to the sequence of nucleotides on
template DNA.
The sequence carried on m -RNA is read in the form
of codons.
A codon is made up of 3 nucleotides
The m-RNA is formed after processing of
heterogeneous nuclear RNA

Biochemistry For Medics 12

Heterogeneous nuclear RNA
(hnRNA)
 In mammalian nuclei , hnRNA is the
immediate product of gene transcription
 The nuclear product is heterogeneous in size
(Variable) and is very large.
Molecular weight may be more than 107, while
the molecular weight of m RNA is less than 2x 106
 75 % of hnRNA is degraded in the nucleus,
only 25% is processed to mature
m RNA

Biochemistry For Medics 13

Heterogeneous nuclear RNA
(hnRNA)

Mature m –RNA is formed from primary transcript by

capping, tailing, splicing and base modification.
Biochemistry For Medics 14
Transfer RNA (t- RNA)
Transfer RNA are the smallest of three major species of
RNA molecules
They have 74-95 nucleotide residues
 They are synthesized by the nuclear processing of a
precursor molecule
They transfer the amino acids from cytoplasm to the
protein synthesizing machinery, hence the name t RNA.
They are easily soluble , hence called “Soluble RNA or s
RNA
They are also called Adapter molecules, since they act as
adapters for the translation of the sequence of nucleotides
of the m RNA in to specific amino acids
There are at least 20 species of t RNA one corresponding
to each of the 20 amino acids required for protein
synthesis.

Biochemistry For Medics 15

Structural characteristics of t- RNA
1) Primary structure- The nucleotide
sequence of all the t RNA molecules allows
extensive intrastand complimentarity that
generates a secondary structure.
2) Secondary structure- Each single t- RNA
shows extensive internal base pairing and
acquires a clover leaf like structure. The
structure is stabilized by hydrogen bonding
between the bases and is a consistent
feature.
Biochemistry For Medics 16
Structural characteristics of t-
RNA
Secondary structure (Clover leaf structure)
All t-RNA contain 5 main arms or loops
which are as follows-
a) Acceptor arm
b) Anticodon arm
c) D HU arm
d) TΨ C arm
e) Extra arm
Biochemistry For Medics 17
Secondary structure of t- RNA
a)Acceptor arm
 The acceptor arm is at 3’ end
 It has 7 base pairs
 The end sequence is unpaired
Cytosine, Cytosine-Adenine at the 3’ end
 The 3’ OH group terminal of Adenine binds with
carboxyl group of amino acids
 The t RNA bound with amino acid is called
Amino acyl t RNA
 CCA attachment is done post transcriptionally

Biochemistry For Medics 18

Secondary structure of t- RNA

The carboxyl group of amino acid is attached to 3’OH group of Adenine

nucleotide of the acceptor arm. The anticodon arm base pairs with the codon
present on the m- RNA
Biochemistry For Medics 19
Secondary structure of t-
RNA(contd.)
b) Anticodon arm
 Lies at the opposite end of acceptor arm
5 base pairs long
Recognizes the triplet codon present in the m
RNA
Base sequence of anticodon arm is
complementary to the base sequence of m RNA
codon.
 Due to complimentarity it can bind specifically
with m RNA by hydrogen bonds.

Biochemistry For Medics 20

Secondary structure of t-
RNA(contd.)
c) DHU arm
 It has 3-4 base pairs
Serves as the recognition site for the enzyme (amino
acyl t RNA synthetase) that adds the amino acid to the
acceptor arm.
d) TΨC arm
This arm is opposite to DHU arm
Since it contains pseudo uridine that is why it is so
named
 It is involved in the binding of t RNA to the ribosomes

Biochemistry For Medics 21

Secondary structure of t-
RNA(contd.)
e) Extra arm or Variable arm
 About 75 % of t RNA molecules possess
a short extra arm
If about 3-5 base pairs are present the
t-RNA is said to be belonging to class 1.
Majority t -RNA belong to class 1.
 The t –RNA belonging to class 2 have
long extra arm, 13-21 base pairs in length.

Biochemistry For Medics 22

Tertiary structure of t- RNA

 The L shaped tertiary

structure is formed by
further folding of the clover
leaf due to hydrogen bonds
between T and D arms.
 The base paired double
helical stems get arranged in
to two double helical
columns, continuous and
perpendicular to one
another.
Biochemistry For Medics 23
Ribosomal RNA (rRNA)
The mammalian ribosome contains two major
nucleoprotein subunits—a larger one with a molecular
weight of 2.8 x 106 (60S) and a smaller subunit with a
molecular weight of 1.4 x 106 (40S).
The 60S subunit contains a 5S ribosomal RNA (rRNA), a
5.8S rRNA, and a 28S rRNA; there are also probably more
than 50 specific polypeptides.
The 40S subunit is smaller and contains a single 18S
rRNA and approximately 30 distinct polypeptide chains.
All of the ribosomal RNA molecules except the 5S rRNA
are processed from a single 45S precursor RNA molecule
in the nucleolus .
5S rRNA is independently transcribed.
Biochemistry For Medics 24
Ribosomal RNA (rRNA)

Biochemistry For Medics 25

Ribosomal RNA (rRNA)
The functions of the ribosomal RNA
molecules in the ribosomal particle are not
fully understood, but they are necessary for
ribosomal assembly and seem to play key
roles in the binding of mRNA to ribosomes
and its translation
Recent studies suggest that an rRNA
component performs the peptidyl transferase
activity and thus is an enzyme (a ribozyme).

Biochemistry For Medics 26

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.

Biochemistry For Medics 27

Small Nuclear RNAs (snRNAs)

snRNAs, a subset of the small RNAs, are

significantly involved in mRNA processing and
gene regulation
Of the several snRNAs, U1, U2, U4, U5, and
U6 are involved in intron removal and the
processing of hnRNA into mRNA
The U7 snRNA is involved in production of
the correct 3' ends of histone mRNA—which
lacks a poly(A) tail.
Biochemistry For Medics 28
Small Nuclear RNAs (snRNAs).

Sn RNA s are involved in the process of splicing (intron removal) of primary

transcript to form mature m RNA. The Sn RNA s form complexes with proteins
to form Ribonucleoprotein particles called snRNPs

Biochemistry For Medics 29

 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

Biochemistry For Medics 30

Micro RNAs (miRNAs)
miRNAs are typically 21–25 nucleotides in
length and are generated by nucleolytic
processing of the products of distinct
genes/transcription units
The small processed mature miRNAs
typically hybridize, via the formation of
imperfect RNA-RNA duplexes within the 3'-
untranslated regions of specific target
mRNAs, leading via unknown mechanisms to
translation arrest.

Biochemistry For Medics 31

Micro RNAs (miRNAs)

microRNAs, short non-coding RNAs present in all living organisms, have

been shown to regulate the expression of at least half of all human
genes. These single-stranded RNAs exert their regulatory action by
binding messenger RNAs and preventing their translation into
proteins.
Biochemistry For Medics 32
Small Interfering RNAs (siRNAs)
 siRNAs are derived by the specific nucleolytic cleavage
of larger, double-stranded RNAs to again form small 21–
25 nucleotide-long products.
These short siRNAs usually form perfect RNA-RNA
hybrids with their distinct targets potentially anywhere
within the length of the mRNA where the complementary
sequence exists.
 Formation of such RNA-RNA duplexes between siRNA
and mRNA results in reduced specific protein production
because the siRNA-mRNA complexes are degraded by
dedicated nucleolytic machinery;
 some or all of this mRNA degradation occurs in specific
organelles termed P bodies.
Biochemistry For Medics 33
Small Interfering RNAs (siRNAs)

Small interfering RNA (siRNA) are 20-25 nucleotide-long double-stranded RNA

molecules that have a variety of roles in the cell. They are involved in the RNA
interference (RNAi) pathway, where it interferes with the expression of a
specific gene by hybridizing to its corresponding RNA sequence in the
target mRNA. This then activates the degrading mRNA. Once the target
mRNA is degraded, the mRNA cannot beFortranslated
Biochemistry Medics into protein. 34
Significance of mi RNAs and si
RNAs
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.
Biochemistry For Medics 35
Summary
RNA exists in several different single-stranded
structures, most of which are directly or indirectly
involved in protein synthesis or its regulation.
The linear array of nucleotides in RNA consists of A, G,
C, and U, and the sugar moiety is ribose.
The major forms of RNA include messenger RNA
(mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA),
and small nuclear RNAs (snRNAs; miRNAs).
 Certain RNA molecules act as catalysts (ribozymes).
miRNAs and siRNAs represent exciting new potential
targets for therapeutic drug development in humans.

Biochemistry For Medics 36