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NUCLEIC ACID-OVERVIEW
PRESENTED BY
Dr. N. Sannigrahi,
Associate Professor,
Department of Botany,
Nistarini College,
Purulia,
D.B. Road, Purulia (W.B)
India
723101
WELCOME TO THE PRESENTATION
CONTENTS:
Nucleotides - Structure and Properties.
Nucleic acid structure – Watson-Crick model of DNA.
Structure of major species of RNA - mRNA, tRNA and rRNA.
Nucleic acid chemistry - UV absorption, effect of acid and alkali
on nucleic acids.
Other functions of nucleotides – Source of energy, component of
coenzymes
NUCLEIC ACID- SOME INTERESTING FACTS
 Life is a three letters word and four letters alphabets with a magic molecule
at the centre-A, T, G, C (Base) and UUU, UAG like many more (Codon).
 Every human being shares 99.9% DNA to everyone,
 If you put all the DNA molecules end to end in your body, the length of the
DNA reach would reach earth to sun and back over 600 times,
 Humans shares 60% genes with the fruit fly, Drosophila melanogoster,
98.7% with Chimpanzee and baboons,
 If you could type 60 words per minute, it would take 50 years to type entire
human genome,
 Nucleic acid is the book of life while gene is the page of the book.
 There are three billion DNA letters in every cell,
 Genes are only make up of 3% of your DNA,
 There is no such thing like ‘Junk Dna’ and it is about 97% of non-coding
sequences,
DNA-DOUBLE HELIX
NUCLEOTIDES - STRUCTURE AND PROPERTIES
 Nucleotides , the energy rich compounds drive all the critical supporting
role of metabolism and act as raw material to build up the genetic
materials-DNA or RNA,
 The segment of DNA that acts as unit of hereditary information and it
undergoes transcription and translation to produce proteins of diverse types
for the cell,
 Each Nucleotides comprise of three structural components-Nitrogen bases,
Pentose sugar and a phosphate; the base and the sugar constitute
nucleoside,
 Bases are two types- Purine and Pyrimidine,
 Each purine base are the derivative of purines nucleus which is fused 6 and
5 member ring, at 4 and 5 carbon positions and have 4 nitrogen atoms at
1,3,7 and 9 position Adenine is 6, amino purine and Guanine is 2 amino, 6
oxypurine.
NUCLEOTIDES - STRUCTURE AND PROPERTIES
 Pyrimidine- Derivatives of parent pyrimidine nucleus which is structurally
a 6, member ring with two nitrogen atoms at 1 and 3 position and 4 carbon
atoms,
 Cytosine is 2, oxy, 6 aminopyrimidine ; Thymine is 5 methyl, 2,6,
dioxypyrimidne; Thymine is 5 methyl 2,6, dioxypyrimidine. Uracil is 2,6
dioxypyurimidine.
 SUGARS:
 Ribose and 2, deoxyribose sugar-two types of sugar are found known as
pentose sugar; have 5 membered ring at their structure.
 When the base condensed with the sugar, a nucleoside is formed like
deoxyadenosine, adenosine, deoxyguanosine and Guanosine.
 In pyrimidine nucleoside, the nitrogen atom at position 3 of the pyrimidine
ring is linked to carbon atom position 1 of the sugar but in purine
nucleoside, the link is between nitrogen atom 9 of purine and carbon atom
1 of the sugar.
 When the pentose sugar residue of a nucleoside is esterified with
phosphoric acid, a nucleotide is formed
NUCLEOTIDES - STRUCTURE AND PROPERTIES
NUCLEIC ACID STRUCTURE – WATSON-CRICK MODEL OF
DNA.
 In the early 1950s, the dark lady of DNA, Rosalind Franklin and Maurice
Wilkins used powerful x-ray diffraction to analyze DNA crystals and shed
light on the structure of DNA. The epoch making discovery of 3D structure
of DNA by Watson and Crick revolutionized the entire domain that
confirmed the following features:
 DNA is present conjugated with histone protein forming
deoxyribonucleoprotein,
 DNA consists of deoxyribose sugar,
 Thymine and Cytosine bases of pyrimidine and Adenine and Guanine bases
of Purine class,
 A phosphate,
 The detail structure of DNA as proposed by Watson and Crick as follows.
NUCLEIC ACID STRUCTURE – WATSON-CRICK MODEL OF DNA.
 Each DNA molecule is composed of two biopolymers strand coiling to
each other,
 Each strand has 5' end ( with a phosphate group) and 3 ' end (with a
hydroxyl group),
 The strands are antiparallel i.e. parallel in nature but opposite in direction,
i. one strand runs in 5 ' direction while other runs in 3 ' direction,
 The diameter of the double helix is 2 nm and the double helix repeats at an
interval of 3.4 nm which corresponds to ten base pairs,
 The two strands are held together by hydrogen bonds and are
complementary to each other,
 The two strands are called polynucleotide as they are made of major
monomer unit, nucleotides. Basically, DNA is composed of the
deoxiribonucleotides ,
 The doxyribonucleotides are joined together by phosphodiester bonds,
 The nitrogen bases that compose the deoxiribonucleotides are A, G, C. T
NUCLEIC ACID STRUCTURE – WATSON-CRICK MODEL OF DNA.
 When G and C are linked, the H bonds formed between their C1-C1, C2-
C2 and C6-C6 positions of the respective opposite bases; the length of the
bonds are 0.292 nm, 0.284 nm and 0.284 nm respectively.
 When A and T are linked, the H bonds are formed between C1-C1 and C6-
C6 positions respectively of the opposite bases. The bond lengths are 0.291
nm and 0.282 nm respectively.
 There are three H bonds between A and T , two bonds between G and C.
although H bonds are very weak, there are so many H bonds which give
stability of the DNA molecule. Therefore, GC DNA is more stable than AT
DNA because of the more H bonds.
 Watson and Crick model; of DNA shows that the vertically stacked bases
inside the double helix would be .34 nm apart and the successive bases i.e.
the pitch of the helix is 3.4 nm and could be accounted for by the presence
of 10 nucleotide residues in each completer turn of the helix. The width of
the DNA helix is 20 Ȧ
CHARGAFF’S RULE OF DNA COMPOSITION
• E. Chargaff and his colleagues (1949) undergone quantitative analysis of
DNA and set the following rules:
 The bases composition of DNA from different species varies from one
another,
 DNAs isolated from different tissues of the same species have the same
base composition,
 The base composition of DNA in any tissue does not change with the age
of the organism , its nutritional status or the changing climate,
 In all species, the DNA has equal number of adenine and thymine residues
(A=T) and equal number of guanine and cytosine (G_=C) residues.
 The quantitative relationships in the DNA analysis is known as Chargaff’s
rule of molar equivalence between the purines and pyrimidine in DNA.
 The ratio of A+T/G+C, known as dissymmetry ratio, varies greatly from
one species of DNA to other and it is characteristic of that species. When
the dissymmetry ratio exceeds one, such DNA is called AT , when the value
is less than one, it is called GC type. The value of dissymmetry ratio in
human being s is 1.4 while Mycobacterium tuberculosis, it is 0.60.
DIFFERENT TYPES OF DNA
 Most of the bacterial and eukaryotic DNA follows Watson and Crick model
known as B-DNA. Beside this, X-ray analysis of DNA crystals at atomic
resolution have revealed that DNA exhibits much more structural diversity
than formerly envisaged. Such variations are
 A-DNA, C-DNA, D-DNA and Z-DNA,
 DNAs with unusual structures are-
 Palindrome DNA, Mirror Repeat, H-DNA, Single stranded DNA etc.
• A-DNA
 DNA assumes B form and under the dehydration condition with reduced
humidity at 75%, with ions of Na, K and Cs, it appears A form because the
phosphate groups in the A-DNA bind fewer water molecules than do
phosphates in B-DNA,
 Right handed helix like B-DNA, vertical rise base pairs is 2.3,
 Number of base air per helical turn is 11, relative to the 3-4Ȧ rise and
10.4Ȧ base pair per turn as B-DNA. Rotation per base pair in A-DNA is
360/11= 32.72º while B-DNA is 360/1.4= 34.61º
DIFFERENT TYPES OF DNA
 C-DNA: It is formed at 60% relative humidity in the presence of Li+ ions,
 This form DNA is right handed with an axis rise of 3.32Ȧ per base pair,
 There are 9.33 base pair per turn of the helix,
 The value of the helix pitch , is, therefore,30.97Ȧ
 The rotation of base pair in C-DNA is 360/9.33= 38.58Ȧ,
 The C-helix has a diameter of 19Ȧ, smaller than that of both A and B-helix,
 The tilt of the base pair is 7.8º
D-DNA:
 It is extremely rare variant with only 8 base pair per helical turn,
 This kind of DNA is found in all DNA molecules devoid of Guanine. By
contrast, A,B,C forms of DNA are found in all DNA molecules irrespective
of their base sequence,
 There is an axial rise of 3.03Ȧ per base pair, with a tilting of 16.7º from the
axis of the helix.
DIFFERENT TYPES OF DNA
DIFFERENT TYPES OF DNA
• Z-DNA:
 Most radical departure from B-DNA characterized by left handed helix,
 Phosphates in the DNA backbone were in a zigzag manner, hence termed
Z-DNA,
 Adjacent sugar residues have alternating orientation and it is because of
this reason that in Z-DNA, the repeating unit is a dinucleotide as against B-
DNA,
 There are 12 base pairs per helical; turn with an axial rise of 3.8Ȧ per base
pair,
 The bases are inclined at 9º with 10.4 in B-DNA,
 The angle twist per repeating unit is 360/12*2=60º as 34.61º per nucleotide
in B-DNA,
 One complete helix is 45.60 in length in contrast 35.36Ȧ in B-DNA,
 The diameter of Z-DNA molecule is 18.4Ȧ whereas 23.7Ȧ in B-DNA.
COMPARATIVE ACCOUNT
Characters A-DNA B-DNA C-DNA Z-DNA
Coupling 75% relative
humidity; Na+,
L+, Cs+
92%, low ion
strength
60% , Li+ Very high salt
conc.
Shape Broadest Intermediate Narrow Narrowest
Helix sense Right handed Right handed Right handed Left handed
Helix diameter 25.5Ȧ 23.7Ȧ 19.0Ȧ 18.4Ȧ
Rise per base
pair
23Ȧ 3.4Ȧ 3.32Ȧ 3.8Ȧ
Base pair/per
turn helix
11 10.4 9.33 12
Helix pitch 25.30Ȧ 35.36Ȧ 30.97Ȧ 45.60Ȧ
DNA WITH UNUSUAL STRUCTURE
• BENT DNA : Some sequence cause bends in the DNA helix,
 Bends are produced whenever 4 or more adenine residues appear
sequentially in one of the two strands,
 Six adenines in a row produce a bend of 18º,
 Bending may be important in the binding of some proteins to DNA,
 Some are the asymmetric sequences that can pair alternatively with a
complementary sequence in the same or opposite strand.
• HAIRPIN: When only a single strand of palindrome DNA is involved,
• CRUCIFORM: When both the strands of double helix DNA is involved.
• PALLINDROMIC DNA :
• Palindrome is a name, word, phase, sentence that leads the same in either
direction like MADAM I’M ADAM,NITIN, LEVEL, ROTATOR,
MALYALAM and many more. Similarly, It is the region of DNA in which
there are inverted repetitions of base sequences occurring over two strands.
Such sequences are complementary within each of the strands and therefore
have the potential to form hairpin loop or cruciform (when both strands of
DNA duplex involved) structures involving intrastrand base pairing.
DNA PALINDROME SEQUENCE
DNA PALINDROME SEQUENCE
• When the inverted sequence occurs within each individual strand of the
DNA, the sequence is called mirror repeat. Mirror repeats do not have
complementary sequences within the same strand and cannot form hairpin
or cruciform structures. Sequences of these types are found virtually every
large DNA molecule and can involve a few or up to thousands of base
units.
• IMPORTANCE:
 Play a significant role in genetic engineering by offering gene cutting and
splicing mechanisms. Restriction endonucleases can identify palindrome
sequence and cut the DNA strands. They mostly cut the DNA sequence
slightly away from the palindrome and between the same nitrogen bases in
both the strands. They are known as ‘sticky ends 'due to their tendency to
easily pair with the complementary strand and form hydrogen bonds.
 DNA replication, gene expression and gene regulation,
 The hairpin formed by the palindrome is vulnerable to breakage and
translocation,
 Play a role in gene expression by methylation.
H-DNA
 H-DNA is an unusual structure, is found in polypyrimidine or polypurine
tracts that also incorporate a mirror repeat within the sequence,
 The pairing and interwinding of three strands of DNA to form a triple
helix,
 Triple helical DNA forms spontaneously only within the long sequences
containing only pyrimidine or only purines in one strand,
 Two of the three strands in the H-DNA triple helix contain pyrimidines and
the third contains purines,
 Both the Palindromes and H-DNA are found in the regulation and
expression of a number of genes in eukaryotes that are recognized by many
specific DNA binding proteins.
H-DNA
STRUCTURE OF MAJOR SPECIES OF RNA - mRNA,
tRNA and rRNA
• RNA:
 RNA like DNA, is a long, unbranched macromolecule consisting of nucleotides
joined by 3 ' ------5 ' phosphodiester bonds,
 number of nucleotides in RNA ranges from a few to 75 to many thousands,
 May be present in free state,
 (0% of RNA present in the cell cytoplasm and 10% in the nucleus,
 Sugar molecule in RNA is ribose sugar that contains a 2 –hydroxyl group,
 The common nitrogen bases are A,U, G.C
 In case of pairing, A pair with U and g with C,
 The sequence of RNA is the same as that of ‘antisense’ strand,
 It need not have complementary base ratio,
 RNAs are of different types-genetic RNA and non-genetic RNA,
 Non-genetic RNAs may be mRNA, tRNA, rRNA, Small nuclear RNA
(snRNA), small cytoplasmic RNA (scRNA), Micro-RNA (miRNA), Small
interfering RNA( siRNA), Guide Rna(gRNA), Short hairpin RNA (shRNA),
Antisense RNA etc.
STRUCTURE OF MAJOR SPECIES OF RNA - mRNA,
tRNA and rRNA
 RNA is alkali-labile,
 RNA stains red with azureph thalate,
 RNA does not act as template for the synthesis,
 RNA usually does not undergo replicate or transcribe,
 RNA generally does not undergo mutation,
 mRNA:
 Major stable form of RNA found in ribosome with highest molecular
weight,
 It is abundant of all types of RNAs and make up to 80% of the total RNA
of a cell,
 Ribosomal RNA represents about 40-60% of the total weight of ribosome,
 The ribosome of prokaryotes and those found in mitochondria and plastids
contain 3 different types of RNAs: 23 sRNA, and 5s RNA of in the larger
sub unit (50S) and 16s RNA of the smaller sub unit (30S),
 Eukaryotes contain 3 kinds of RNA: 28s RNA, and 5S RNA in the larger
unit (60S) and 18s RNA in the smaller sub unit (40s).
STRUCTURE OF MAJOR SPECIES OF RNA - mRNA,
tRNA and rRNA
 mRNA is most heterogeneous in size and stability among all types of
RNAs,
 It has base sequence complementary to DNA and carries genetic
information or ‘message’ for the assembly of amino acids from DNA to
ribosome, the site of protein synthesis,
 In prokaryotes cells, mRNA is metabolically unstable with high turnover
rate whereas it is rather stable in eukaryotes ,
 It is synthesized by DNA –dependent RNA polymerase,
 If mRNA carries the codes for the synthesis of simple protein molecular, it
is called monocistronic and if it codes for more than one kind of protein, it
is known as polycistronic type as in E.coli.
 mRNAs in bacterial systems with half life from a few seconds to 2 minutes
but in eukaryotes, it is ranging from few hours to one day (Half life= the
period of time after which the half is degraded).
DNA →mRNA →PROTEIN
STRUCTURE OF MAJOR SPECIES OF RNA - mRNA, tRNA and
rRNA
 mRNAs are single stranded and complementary to the sense strand of their
respective structural genes, Both types of mRNA molecules are synthesized
with a triphosphate group at the 5 ' end and protein synthesis begins at the
start codon near 5 ' end of the mRNA,
 The other end of mRNA molecules, 3 ' hydroxyl end, has attached a
polymer of adenylate residues, 20-250 nucleotides in length,
 mRNA also codes initiation codon -AUG or GUG and termination codon -
UAA, UAG or UGA along with more triplet codes as far as the structural
gene is concerned,
 The mRNA is being short lived is dismantled immediately after it has been
used for the synthesis of particular protein for which it is short lived,
 The mRNA acts as template for the translation without following any
grammatical syntax.
 Thus, the language of DNA is translated into the voice of protein through
the central dogma-transcription and translation.
STRUCTURE OF MAJOR SPECIES OF RNA - mRNA,
tRNA and rRNA
• tRNA: It is the smallest polymeric form of RNA, seem to be generated by
the nuclear processing of a precursor molecule,
• 15% of the total RNA of cell,
• It is often called soluble RNA as it remains dissolved in solution after
centrifuging a broken cell,
• Mostly acts as specific carriers of activated amino acids to a specific site on
the protein synthesizing template,
• In bacterial cells, there are more than 70 tRNAs and in eukaryotes, the
number is even greater because of mitochondria and chloroplast,
• tRNA has 4S value and length of 70-85 nucleotides which is folded over
itself forming clover leaf like structure (Holley et al, 1964, two
dimensional) or L-shaped (Klug, three dimensional structure),
• STYRUCTURE
• Four main arms or sites excluding a fifth small arm called extra arm or
blind lump,
STRUCTURE OF MAJOR SPECIES OF RNA - mRNA,
tRNA and rRNA
• The four arms or sites are-
• Acceptor arm or amino acid binding site having CCA-OH 3 ' end and G-P
5 ' end. The specific amino acid binds at 3 ' end.
• Anticodon site or Loop: Present on the acceptor arm, anticodon is triplet,
unpaired bases which binds with the codon of mRNA in a complementary
manner. e.g. anticodon GAA binds with the codon of CUU and it carries
amino acid, leucine at the amino acid binding site.
• Aminoacyl Synthetase Binding Loop (DHU arm) :The dihydrouridine
(DHU) loops binds with aminoacyl -tRNA synthetase, the amino acid
activating enzyme, loop has 8-12 base pairs; 20 such amino acids and 20
such enzymes at least in each cell.
• Ribosomal Binding Loop ( TφC Loop): The fourth active site opposite to
DHU loop which recognizes a ribosome which binds the tRNA in such a
manner that facilitates codon-anticodon pairing. This loop has 7 base pairs.
• The different arm regions hydrogen bonding between the nitrogen bases.
tRNA- CLOVER LEAF STRUCTURE
STRUCTURE OF MAJOR SPECIES OF RNA - mRNA,
tRNA and rRNA
• tRNA acts as vehicle to pick up amino acids scattered throughout the
cytosol and transport them to specific codons of mRNA molecules on
ribosome,
• There are at least one specific tRNA for each amino acids and some amino
acids may have 2-6 specific t-RNAs according to the anticodon,
• All t-RNA molecules have unique similarity i.e. the overall distance from
CCA at one end to the anticodon at the other end is constant. The difference
in nucleotide numbers in various tRNA molecules is, in fact, compensated
for by the size of the “extra arm”, which is located between the anticodon
loop and Tφ C loop.
• All tRNA molecules are unbranched chains containing 73-93
ribonucleotide residues, corresponding to molecular weight between 24000
and 31000.
• About 50% of the nucleotides in tRNAs are paired to form double helices.
FUNCTION OF DNA
i. DNA is the genetic material of all living organisms except virus.
ii. It is the store house of genetic information and responsible for the
transmission from one generation to the other,
iii. It has an autocatalytic function i.e. capacity for replication mostly by the
semi-replication procedure although dispersive or other methods exist,
iv. It has a heterocatalytic function i.e. it can produce dissimilar molecules like
RNA, protein s by transcription and translation respectively. More precisely,
transcription involves formation of RNA from DNA whereas translation
involves the formation of proteins as per the code of the mRNA.
v. The gene products are enzymes that catalyses the biochemical reactions of
cell,
vi. DNA, as it contains genes , govern all phenotypic characters of organisms,
vii. The process of differentiation is governed by ands regulated by DNA,
viii. If DNA is damaged, it can repair itself so that the genetic information is
preserved,
ix. DNA has possibility of variations by recombination and mutations.
STRUCTURE OF MAJOR SPECIES OF RNA - mRNA,
tRNA and rRNA
 Ribosomal RNA (rRNA) or Insoluble RNA:
 Most stable form of RNA found in ribosome with highest molecular weight,
 It is abundant of all types of RNAs and make up about 80% of the total RNA of
a cell,
 Ribosomal RNA represents about 40-60% of the total weight of ribosome,
 The ribosome of prokaryotes and eukaryotes cell possess different species of
RNA ; for prokaryotes along with mitochondria and plastid, 3 different types of
RNA: 23s RNA and 5s RNA in the larger subunit (50S) and 16s RNA in the
smaller subunit (30s) subunit; eukaryotes cell also contains 3 kinds of RNA:
28s RNA and 5sRNA in the larger (60S) and 18s RNA in the smaller (40s)
subunit.
 rRNA from all sources has G-C contents more than 50%,
 rRNA molecule appears as a single unbranched polynucleotide strand
(=Primary structure).At low ionic strength, the molecule reveals the presence of
compact helical regions with complementary pairing and looped outer regions.
RIBOSOMAL RNA ( rRNA)
STRUCTURE OF MAJOR SPECIES OF RNA - mRNA,
tRNA and rRNA
• rRNA is involved in protein synthesis,
• Different types of rRNAs have different specific functions, e.g. 18sRNA
provides binding site to mRNA and 5s RNA has similar role to tRNA,
• In some cases, rRNA may have hair pin like structure.
• Besides the mRNA, tRNA and rRNA, there are different other types of
RNAs present in the cell system to perform manifold molecular activities in
order to keep up the cellular regulation and sustainability for cellular
vitality and dynamism.
SOME OTHER TYPES OF RNAs
• Small Nuclear RNA (snRNA): Small Uridine rich RNA that occurs inside
the nucleus. It is associated with 7-8 molecules of proteins and take part in
splicing and processing of other RNAs.
• Small Cytoplasmic RNA (scRNA): It is also small RNA present in the
cytoplasm. It helps in processing of polypeptides.
• Micro-RNA (miRNA): Small, non-coding RNA molecule containing about
22 nucleotides and found in plants, animals and some viruses. It functions
in mRNA silencing and post transcriptional regulation of gene expression.
The human genome may encode over 1000 miRNAs.
• Small Interfering RNAs (siRNA): The siRNA are derived from longer
regions of double stranded RNA.
• Guide RNA (gRNA): Synthesized from mtDNA and used for RNA editing.
• Short Hairpin RNA ( shRNA): In artificial RNA used for gene silencing.
• Antisense RNA: Inhibit translation process during protein synthesis.
FUNCTIONS OF RNA
 Genomic or Genetic RNA: Carry the hereditary information in riboviruses
and viriods,
 RNA as primer- acts as primer in DNA replication,
 In Ribosome- RRNAs are their constituents of ribosome,
 Role in genetic code- mRNA contains the codon the carry genetic messages
from DNA by transcription which are translated into the language of
proteins,
 Protein synthesis-All the three type of RNAs take part in the biosynthesis
of proteins which are transformed into the protoplasmic structures along
with diverse set of enzymes,
 Polypeptidyl Processing-It is carried out by small cytoplasmic RNA (
scRNAs),
 Ribozyme - a non-protein enzyme is made up of RNAs , Ribonuclease-P
and peptidyltransaferase enzymes are also made up of RNAs,
 RNA processing- snRNA participate in splicing and processing of RNAs.
Nucleic acid chemistry - UV absorption, effect of acid and
alkali on nucleic acids.
 UV RADIATION is a part of electromagnetic radiation that lies between
200-400 nm, with shorter wavelength between violet and visible spectrum.
The range is further sub-divided into short wave (200-280 nm , UV-
C),middle wave (280-320, UV-B), and long wave (320-400 nm, UV-A) of
light.
 UV-C is very dangerous and lethal .It causes the DNA damage via two
distinct type of mutations- Dimerizing mutations and Oxidative mutations
 In fact, UV-A radiation commonly damages DNA in an oxygen-dependent
manner that involves photosensitization. This leads to the production of a
free radical that then interacts with and oxidizes DNA bases. These
oxidized bases don't pair correctly during replication, resulting in
mutations.
 One example: G to T transversion mediated by reactive oxygen species
(ROS). The oxidation of Guanine into 8-Oxyguanine prevents the hydrogen
bonding required to base pair with Cytosine. Instead during replication, 8-
Oxyguanine can base pair with Adenine via two hydrogen bonds. When the
EFFECT OF UV ON DNA
• Strand is synthesized, the base position originally occupied by a Guanine is
replaced with a Thiamine , leading to a G to T transversion Oxidative
mutation can results in single strand break.
• DIMERIZING MUTATIONS: exposure to UV-B and lesser extent of
UV-A leads to the formation of common photochemical products in DNA-
Cyclobutane pyrimidine dimmers (CPD)as well as Pyrimidine (6-
4)pyrimidone photoproducts(64pps).CPDs formed when two adjacent
pyrimidine (thymine, TT or Cytosine, CC) become covalently linked by
their C=C bonds. These four carbons form a cyclic ring (Cyclobutane) that
links the two pyrimidine, thus creating a chemical intermediate not
normally found in DNA.The photochemical product cause a kick in the
DNA that prevents the Pyrimidine base pairing and prevents DNA
replication. Unlike oxidative mutations, UV induced dimerized mutations
arise from the direct absorption of UV photons.
EFFECT OF UV ON DNA
EFFECT OF pH ON DNA
 Nucleic acids are acidic because of the presence of phosphate group along
with the proton which is easily lost.
 The stability of DNA is governed mainly by the two factors-the two strands
double helix along with the base pairing among complementary strands as
well as the stacking present in between the neighboring nucleotides.
 Non-physiological factors like temperature , pH, ionic strength break the
DNA helix and cause conformational change even though the DNA is
relatively stable in the aqueous solution.
 In a neutral pH range, pH 5 to 9, DNA molecules are quite stable. However,
if the pH becomes too acidic or alkaline, DNA molecules are prone to
destabilization. At pH 5 or lower, DNA is liable to depurination (i.e. the
loss of purine bases from DNA).
 DNA is sensitive to alkaline denaturation at high pH at 9.0 because of
hydroxides present . These negatively charged ions denature DNA strands
by disrupting hydrogen bonds among them.
EFFECT OF pH ON DNA
EFFECT OF pH ON DNA
• Unlike RNA, each sugar group of DNA lacks hydroxyl group at 2' position.
Because of the difference, DNA substantially more stable in the alkali
solution.
• Acidic pH stabilizes crucial intermolecular and intramolecular RNA bonds,
including those important for protein synthesis evolution and promotes
extra protonated base interactions, allowing RNA to behave under these
settings without being bound by traditional base pairing constraints.
• So, from the above observation, it is quite clear that the different physical
parameters like UV ray, acid, alkali have stron impact upon the stability of
the DNA structure.
• The different kind of the physical factors like metal ions along with the
other parameters are employed to undertake the different experimental
procedure in the domain of nucleic acid.
OTHER FUNCTIONS OF NUCLEOTIDES – SOURCE OF
ENERGY, COMPONENT OF COENZYMES
 Nucleotide compounds play significant role in the physiological activities
of the living organisms.
 ATP plays significant role in energy metabolism. The energy release and
absorption in the body is mainly reflected by the production and
consumption of ATP.
 They provide chemical energy beside in the form of the nucleoside
triphosphates, adenosine triphosphate (ATP), guanosine triphosphate
(GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP)—
throughout the cell for the many cellular functions that demand energy,
including: amino acid, protein and cell membrane .
 Metabolism of some substances along with adenylate is also acts as a
component of some coenzymes like coenzyme I, II and coenzyme A.
 Besides, cyclic nucleotides have certain regulatory effect on many basic
biological processes.
THANKS FOR YOUR HAPPINESS
• ACKNOWLEDGEMENT:
 Cell and Molecular Biology- Ajoy Paul,
 National Institute of Health website,
 Khan Academy,
 Google for images,
 Different web pages for the content,
 Different others for directly or indirectly associated with this presentation.
• Disclaimer:
 This presentation has been developed for the academic fraternity as a
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Nucleic Acid-its structural and functional complexity.

  • 1. NUCLEIC ACID-OVERVIEW PRESENTED BY Dr. N. Sannigrahi, Associate Professor, Department of Botany, Nistarini College, Purulia, D.B. Road, Purulia (W.B) India 723101
  • 2. WELCOME TO THE PRESENTATION CONTENTS: Nucleotides - Structure and Properties. Nucleic acid structure – Watson-Crick model of DNA. Structure of major species of RNA - mRNA, tRNA and rRNA. Nucleic acid chemistry - UV absorption, effect of acid and alkali on nucleic acids. Other functions of nucleotides – Source of energy, component of coenzymes
  • 3. NUCLEIC ACID- SOME INTERESTING FACTS  Life is a three letters word and four letters alphabets with a magic molecule at the centre-A, T, G, C (Base) and UUU, UAG like many more (Codon).  Every human being shares 99.9% DNA to everyone,  If you put all the DNA molecules end to end in your body, the length of the DNA reach would reach earth to sun and back over 600 times,  Humans shares 60% genes with the fruit fly, Drosophila melanogoster, 98.7% with Chimpanzee and baboons,  If you could type 60 words per minute, it would take 50 years to type entire human genome,  Nucleic acid is the book of life while gene is the page of the book.  There are three billion DNA letters in every cell,  Genes are only make up of 3% of your DNA,  There is no such thing like ‘Junk Dna’ and it is about 97% of non-coding sequences,
  • 5. NUCLEOTIDES - STRUCTURE AND PROPERTIES  Nucleotides , the energy rich compounds drive all the critical supporting role of metabolism and act as raw material to build up the genetic materials-DNA or RNA,  The segment of DNA that acts as unit of hereditary information and it undergoes transcription and translation to produce proteins of diverse types for the cell,  Each Nucleotides comprise of three structural components-Nitrogen bases, Pentose sugar and a phosphate; the base and the sugar constitute nucleoside,  Bases are two types- Purine and Pyrimidine,  Each purine base are the derivative of purines nucleus which is fused 6 and 5 member ring, at 4 and 5 carbon positions and have 4 nitrogen atoms at 1,3,7 and 9 position Adenine is 6, amino purine and Guanine is 2 amino, 6 oxypurine.
  • 6. NUCLEOTIDES - STRUCTURE AND PROPERTIES
  • 7.  Pyrimidine- Derivatives of parent pyrimidine nucleus which is structurally a 6, member ring with two nitrogen atoms at 1 and 3 position and 4 carbon atoms,  Cytosine is 2, oxy, 6 aminopyrimidine ; Thymine is 5 methyl, 2,6, dioxypyrimidne; Thymine is 5 methyl 2,6, dioxypyrimidine. Uracil is 2,6 dioxypyurimidine.  SUGARS:  Ribose and 2, deoxyribose sugar-two types of sugar are found known as pentose sugar; have 5 membered ring at their structure.  When the base condensed with the sugar, a nucleoside is formed like deoxyadenosine, adenosine, deoxyguanosine and Guanosine.  In pyrimidine nucleoside, the nitrogen atom at position 3 of the pyrimidine ring is linked to carbon atom position 1 of the sugar but in purine nucleoside, the link is between nitrogen atom 9 of purine and carbon atom 1 of the sugar.  When the pentose sugar residue of a nucleoside is esterified with phosphoric acid, a nucleotide is formed
  • 8. NUCLEOTIDES - STRUCTURE AND PROPERTIES
  • 9. NUCLEIC ACID STRUCTURE – WATSON-CRICK MODEL OF DNA.  In the early 1950s, the dark lady of DNA, Rosalind Franklin and Maurice Wilkins used powerful x-ray diffraction to analyze DNA crystals and shed light on the structure of DNA. The epoch making discovery of 3D structure of DNA by Watson and Crick revolutionized the entire domain that confirmed the following features:  DNA is present conjugated with histone protein forming deoxyribonucleoprotein,  DNA consists of deoxyribose sugar,  Thymine and Cytosine bases of pyrimidine and Adenine and Guanine bases of Purine class,  A phosphate,  The detail structure of DNA as proposed by Watson and Crick as follows.
  • 10. NUCLEIC ACID STRUCTURE – WATSON-CRICK MODEL OF DNA.  Each DNA molecule is composed of two biopolymers strand coiling to each other,  Each strand has 5' end ( with a phosphate group) and 3 ' end (with a hydroxyl group),  The strands are antiparallel i.e. parallel in nature but opposite in direction, i. one strand runs in 5 ' direction while other runs in 3 ' direction,  The diameter of the double helix is 2 nm and the double helix repeats at an interval of 3.4 nm which corresponds to ten base pairs,  The two strands are held together by hydrogen bonds and are complementary to each other,  The two strands are called polynucleotide as they are made of major monomer unit, nucleotides. Basically, DNA is composed of the deoxiribonucleotides ,  The doxyribonucleotides are joined together by phosphodiester bonds,  The nitrogen bases that compose the deoxiribonucleotides are A, G, C. T
  • 11. NUCLEIC ACID STRUCTURE – WATSON-CRICK MODEL OF DNA.  When G and C are linked, the H bonds formed between their C1-C1, C2- C2 and C6-C6 positions of the respective opposite bases; the length of the bonds are 0.292 nm, 0.284 nm and 0.284 nm respectively.  When A and T are linked, the H bonds are formed between C1-C1 and C6- C6 positions respectively of the opposite bases. The bond lengths are 0.291 nm and 0.282 nm respectively.  There are three H bonds between A and T , two bonds between G and C. although H bonds are very weak, there are so many H bonds which give stability of the DNA molecule. Therefore, GC DNA is more stable than AT DNA because of the more H bonds.  Watson and Crick model; of DNA shows that the vertically stacked bases inside the double helix would be .34 nm apart and the successive bases i.e. the pitch of the helix is 3.4 nm and could be accounted for by the presence of 10 nucleotide residues in each completer turn of the helix. The width of the DNA helix is 20 Ȧ
  • 12. CHARGAFF’S RULE OF DNA COMPOSITION • E. Chargaff and his colleagues (1949) undergone quantitative analysis of DNA and set the following rules:  The bases composition of DNA from different species varies from one another,  DNAs isolated from different tissues of the same species have the same base composition,  The base composition of DNA in any tissue does not change with the age of the organism , its nutritional status or the changing climate,  In all species, the DNA has equal number of adenine and thymine residues (A=T) and equal number of guanine and cytosine (G_=C) residues.  The quantitative relationships in the DNA analysis is known as Chargaff’s rule of molar equivalence between the purines and pyrimidine in DNA.  The ratio of A+T/G+C, known as dissymmetry ratio, varies greatly from one species of DNA to other and it is characteristic of that species. When the dissymmetry ratio exceeds one, such DNA is called AT , when the value is less than one, it is called GC type. The value of dissymmetry ratio in human being s is 1.4 while Mycobacterium tuberculosis, it is 0.60.
  • 13. DIFFERENT TYPES OF DNA  Most of the bacterial and eukaryotic DNA follows Watson and Crick model known as B-DNA. Beside this, X-ray analysis of DNA crystals at atomic resolution have revealed that DNA exhibits much more structural diversity than formerly envisaged. Such variations are  A-DNA, C-DNA, D-DNA and Z-DNA,  DNAs with unusual structures are-  Palindrome DNA, Mirror Repeat, H-DNA, Single stranded DNA etc. • A-DNA  DNA assumes B form and under the dehydration condition with reduced humidity at 75%, with ions of Na, K and Cs, it appears A form because the phosphate groups in the A-DNA bind fewer water molecules than do phosphates in B-DNA,  Right handed helix like B-DNA, vertical rise base pairs is 2.3,  Number of base air per helical turn is 11, relative to the 3-4Ȧ rise and 10.4Ȧ base pair per turn as B-DNA. Rotation per base pair in A-DNA is 360/11= 32.72º while B-DNA is 360/1.4= 34.61º
  • 14. DIFFERENT TYPES OF DNA  C-DNA: It is formed at 60% relative humidity in the presence of Li+ ions,  This form DNA is right handed with an axis rise of 3.32Ȧ per base pair,  There are 9.33 base pair per turn of the helix,  The value of the helix pitch , is, therefore,30.97Ȧ  The rotation of base pair in C-DNA is 360/9.33= 38.58Ȧ,  The C-helix has a diameter of 19Ȧ, smaller than that of both A and B-helix,  The tilt of the base pair is 7.8º D-DNA:  It is extremely rare variant with only 8 base pair per helical turn,  This kind of DNA is found in all DNA molecules devoid of Guanine. By contrast, A,B,C forms of DNA are found in all DNA molecules irrespective of their base sequence,  There is an axial rise of 3.03Ȧ per base pair, with a tilting of 16.7º from the axis of the helix.
  • 16. DIFFERENT TYPES OF DNA • Z-DNA:  Most radical departure from B-DNA characterized by left handed helix,  Phosphates in the DNA backbone were in a zigzag manner, hence termed Z-DNA,  Adjacent sugar residues have alternating orientation and it is because of this reason that in Z-DNA, the repeating unit is a dinucleotide as against B- DNA,  There are 12 base pairs per helical; turn with an axial rise of 3.8Ȧ per base pair,  The bases are inclined at 9º with 10.4 in B-DNA,  The angle twist per repeating unit is 360/12*2=60º as 34.61º per nucleotide in B-DNA,  One complete helix is 45.60 in length in contrast 35.36Ȧ in B-DNA,  The diameter of Z-DNA molecule is 18.4Ȧ whereas 23.7Ȧ in B-DNA.
  • 17. COMPARATIVE ACCOUNT Characters A-DNA B-DNA C-DNA Z-DNA Coupling 75% relative humidity; Na+, L+, Cs+ 92%, low ion strength 60% , Li+ Very high salt conc. Shape Broadest Intermediate Narrow Narrowest Helix sense Right handed Right handed Right handed Left handed Helix diameter 25.5Ȧ 23.7Ȧ 19.0Ȧ 18.4Ȧ Rise per base pair 23Ȧ 3.4Ȧ 3.32Ȧ 3.8Ȧ Base pair/per turn helix 11 10.4 9.33 12 Helix pitch 25.30Ȧ 35.36Ȧ 30.97Ȧ 45.60Ȧ
  • 18. DNA WITH UNUSUAL STRUCTURE • BENT DNA : Some sequence cause bends in the DNA helix,  Bends are produced whenever 4 or more adenine residues appear sequentially in one of the two strands,  Six adenines in a row produce a bend of 18º,  Bending may be important in the binding of some proteins to DNA,  Some are the asymmetric sequences that can pair alternatively with a complementary sequence in the same or opposite strand. • HAIRPIN: When only a single strand of palindrome DNA is involved, • CRUCIFORM: When both the strands of double helix DNA is involved. • PALLINDROMIC DNA : • Palindrome is a name, word, phase, sentence that leads the same in either direction like MADAM I’M ADAM,NITIN, LEVEL, ROTATOR, MALYALAM and many more. Similarly, It is the region of DNA in which there are inverted repetitions of base sequences occurring over two strands. Such sequences are complementary within each of the strands and therefore have the potential to form hairpin loop or cruciform (when both strands of DNA duplex involved) structures involving intrastrand base pairing.
  • 20. DNA PALINDROME SEQUENCE • When the inverted sequence occurs within each individual strand of the DNA, the sequence is called mirror repeat. Mirror repeats do not have complementary sequences within the same strand and cannot form hairpin or cruciform structures. Sequences of these types are found virtually every large DNA molecule and can involve a few or up to thousands of base units. • IMPORTANCE:  Play a significant role in genetic engineering by offering gene cutting and splicing mechanisms. Restriction endonucleases can identify palindrome sequence and cut the DNA strands. They mostly cut the DNA sequence slightly away from the palindrome and between the same nitrogen bases in both the strands. They are known as ‘sticky ends 'due to their tendency to easily pair with the complementary strand and form hydrogen bonds.  DNA replication, gene expression and gene regulation,  The hairpin formed by the palindrome is vulnerable to breakage and translocation,  Play a role in gene expression by methylation.
  • 21. H-DNA  H-DNA is an unusual structure, is found in polypyrimidine or polypurine tracts that also incorporate a mirror repeat within the sequence,  The pairing and interwinding of three strands of DNA to form a triple helix,  Triple helical DNA forms spontaneously only within the long sequences containing only pyrimidine or only purines in one strand,  Two of the three strands in the H-DNA triple helix contain pyrimidines and the third contains purines,  Both the Palindromes and H-DNA are found in the regulation and expression of a number of genes in eukaryotes that are recognized by many specific DNA binding proteins.
  • 22. H-DNA
  • 23. STRUCTURE OF MAJOR SPECIES OF RNA - mRNA, tRNA and rRNA • RNA:  RNA like DNA, is a long, unbranched macromolecule consisting of nucleotides joined by 3 ' ------5 ' phosphodiester bonds,  number of nucleotides in RNA ranges from a few to 75 to many thousands,  May be present in free state,  (0% of RNA present in the cell cytoplasm and 10% in the nucleus,  Sugar molecule in RNA is ribose sugar that contains a 2 –hydroxyl group,  The common nitrogen bases are A,U, G.C  In case of pairing, A pair with U and g with C,  The sequence of RNA is the same as that of ‘antisense’ strand,  It need not have complementary base ratio,  RNAs are of different types-genetic RNA and non-genetic RNA,  Non-genetic RNAs may be mRNA, tRNA, rRNA, Small nuclear RNA (snRNA), small cytoplasmic RNA (scRNA), Micro-RNA (miRNA), Small interfering RNA( siRNA), Guide Rna(gRNA), Short hairpin RNA (shRNA), Antisense RNA etc.
  • 24. STRUCTURE OF MAJOR SPECIES OF RNA - mRNA, tRNA and rRNA  RNA is alkali-labile,  RNA stains red with azureph thalate,  RNA does not act as template for the synthesis,  RNA usually does not undergo replicate or transcribe,  RNA generally does not undergo mutation,  mRNA:  Major stable form of RNA found in ribosome with highest molecular weight,  It is abundant of all types of RNAs and make up to 80% of the total RNA of a cell,  Ribosomal RNA represents about 40-60% of the total weight of ribosome,  The ribosome of prokaryotes and those found in mitochondria and plastids contain 3 different types of RNAs: 23 sRNA, and 5s RNA of in the larger sub unit (50S) and 16s RNA of the smaller sub unit (30S),  Eukaryotes contain 3 kinds of RNA: 28s RNA, and 5S RNA in the larger unit (60S) and 18s RNA in the smaller sub unit (40s).
  • 25. STRUCTURE OF MAJOR SPECIES OF RNA - mRNA, tRNA and rRNA  mRNA is most heterogeneous in size and stability among all types of RNAs,  It has base sequence complementary to DNA and carries genetic information or ‘message’ for the assembly of amino acids from DNA to ribosome, the site of protein synthesis,  In prokaryotes cells, mRNA is metabolically unstable with high turnover rate whereas it is rather stable in eukaryotes ,  It is synthesized by DNA –dependent RNA polymerase,  If mRNA carries the codes for the synthesis of simple protein molecular, it is called monocistronic and if it codes for more than one kind of protein, it is known as polycistronic type as in E.coli.  mRNAs in bacterial systems with half life from a few seconds to 2 minutes but in eukaryotes, it is ranging from few hours to one day (Half life= the period of time after which the half is degraded).
  • 27. STRUCTURE OF MAJOR SPECIES OF RNA - mRNA, tRNA and rRNA  mRNAs are single stranded and complementary to the sense strand of their respective structural genes, Both types of mRNA molecules are synthesized with a triphosphate group at the 5 ' end and protein synthesis begins at the start codon near 5 ' end of the mRNA,  The other end of mRNA molecules, 3 ' hydroxyl end, has attached a polymer of adenylate residues, 20-250 nucleotides in length,  mRNA also codes initiation codon -AUG or GUG and termination codon - UAA, UAG or UGA along with more triplet codes as far as the structural gene is concerned,  The mRNA is being short lived is dismantled immediately after it has been used for the synthesis of particular protein for which it is short lived,  The mRNA acts as template for the translation without following any grammatical syntax.  Thus, the language of DNA is translated into the voice of protein through the central dogma-transcription and translation.
  • 28. STRUCTURE OF MAJOR SPECIES OF RNA - mRNA, tRNA and rRNA • tRNA: It is the smallest polymeric form of RNA, seem to be generated by the nuclear processing of a precursor molecule, • 15% of the total RNA of cell, • It is often called soluble RNA as it remains dissolved in solution after centrifuging a broken cell, • Mostly acts as specific carriers of activated amino acids to a specific site on the protein synthesizing template, • In bacterial cells, there are more than 70 tRNAs and in eukaryotes, the number is even greater because of mitochondria and chloroplast, • tRNA has 4S value and length of 70-85 nucleotides which is folded over itself forming clover leaf like structure (Holley et al, 1964, two dimensional) or L-shaped (Klug, three dimensional structure), • STYRUCTURE • Four main arms or sites excluding a fifth small arm called extra arm or blind lump,
  • 29. STRUCTURE OF MAJOR SPECIES OF RNA - mRNA, tRNA and rRNA • The four arms or sites are- • Acceptor arm or amino acid binding site having CCA-OH 3 ' end and G-P 5 ' end. The specific amino acid binds at 3 ' end. • Anticodon site or Loop: Present on the acceptor arm, anticodon is triplet, unpaired bases which binds with the codon of mRNA in a complementary manner. e.g. anticodon GAA binds with the codon of CUU and it carries amino acid, leucine at the amino acid binding site. • Aminoacyl Synthetase Binding Loop (DHU arm) :The dihydrouridine (DHU) loops binds with aminoacyl -tRNA synthetase, the amino acid activating enzyme, loop has 8-12 base pairs; 20 such amino acids and 20 such enzymes at least in each cell. • Ribosomal Binding Loop ( TφC Loop): The fourth active site opposite to DHU loop which recognizes a ribosome which binds the tRNA in such a manner that facilitates codon-anticodon pairing. This loop has 7 base pairs. • The different arm regions hydrogen bonding between the nitrogen bases.
  • 30. tRNA- CLOVER LEAF STRUCTURE
  • 31. STRUCTURE OF MAJOR SPECIES OF RNA - mRNA, tRNA and rRNA • tRNA acts as vehicle to pick up amino acids scattered throughout the cytosol and transport them to specific codons of mRNA molecules on ribosome, • There are at least one specific tRNA for each amino acids and some amino acids may have 2-6 specific t-RNAs according to the anticodon, • All t-RNA molecules have unique similarity i.e. the overall distance from CCA at one end to the anticodon at the other end is constant. The difference in nucleotide numbers in various tRNA molecules is, in fact, compensated for by the size of the “extra arm”, which is located between the anticodon loop and Tφ C loop. • All tRNA molecules are unbranched chains containing 73-93 ribonucleotide residues, corresponding to molecular weight between 24000 and 31000. • About 50% of the nucleotides in tRNAs are paired to form double helices.
  • 32. FUNCTION OF DNA i. DNA is the genetic material of all living organisms except virus. ii. It is the store house of genetic information and responsible for the transmission from one generation to the other, iii. It has an autocatalytic function i.e. capacity for replication mostly by the semi-replication procedure although dispersive or other methods exist, iv. It has a heterocatalytic function i.e. it can produce dissimilar molecules like RNA, protein s by transcription and translation respectively. More precisely, transcription involves formation of RNA from DNA whereas translation involves the formation of proteins as per the code of the mRNA. v. The gene products are enzymes that catalyses the biochemical reactions of cell, vi. DNA, as it contains genes , govern all phenotypic characters of organisms, vii. The process of differentiation is governed by ands regulated by DNA, viii. If DNA is damaged, it can repair itself so that the genetic information is preserved, ix. DNA has possibility of variations by recombination and mutations.
  • 33. STRUCTURE OF MAJOR SPECIES OF RNA - mRNA, tRNA and rRNA  Ribosomal RNA (rRNA) or Insoluble RNA:  Most stable form of RNA found in ribosome with highest molecular weight,  It is abundant of all types of RNAs and make up about 80% of the total RNA of a cell,  Ribosomal RNA represents about 40-60% of the total weight of ribosome,  The ribosome of prokaryotes and eukaryotes cell possess different species of RNA ; for prokaryotes along with mitochondria and plastid, 3 different types of RNA: 23s RNA and 5s RNA in the larger subunit (50S) and 16s RNA in the smaller subunit (30s) subunit; eukaryotes cell also contains 3 kinds of RNA: 28s RNA and 5sRNA in the larger (60S) and 18s RNA in the smaller (40s) subunit.  rRNA from all sources has G-C contents more than 50%,  rRNA molecule appears as a single unbranched polynucleotide strand (=Primary structure).At low ionic strength, the molecule reveals the presence of compact helical regions with complementary pairing and looped outer regions.
  • 35. STRUCTURE OF MAJOR SPECIES OF RNA - mRNA, tRNA and rRNA • rRNA is involved in protein synthesis, • Different types of rRNAs have different specific functions, e.g. 18sRNA provides binding site to mRNA and 5s RNA has similar role to tRNA, • In some cases, rRNA may have hair pin like structure. • Besides the mRNA, tRNA and rRNA, there are different other types of RNAs present in the cell system to perform manifold molecular activities in order to keep up the cellular regulation and sustainability for cellular vitality and dynamism.
  • 36. SOME OTHER TYPES OF RNAs • Small Nuclear RNA (snRNA): Small Uridine rich RNA that occurs inside the nucleus. It is associated with 7-8 molecules of proteins and take part in splicing and processing of other RNAs. • Small Cytoplasmic RNA (scRNA): It is also small RNA present in the cytoplasm. It helps in processing of polypeptides. • Micro-RNA (miRNA): Small, non-coding RNA molecule containing about 22 nucleotides and found in plants, animals and some viruses. It functions in mRNA silencing and post transcriptional regulation of gene expression. The human genome may encode over 1000 miRNAs. • Small Interfering RNAs (siRNA): The siRNA are derived from longer regions of double stranded RNA. • Guide RNA (gRNA): Synthesized from mtDNA and used for RNA editing. • Short Hairpin RNA ( shRNA): In artificial RNA used for gene silencing. • Antisense RNA: Inhibit translation process during protein synthesis.
  • 37. FUNCTIONS OF RNA  Genomic or Genetic RNA: Carry the hereditary information in riboviruses and viriods,  RNA as primer- acts as primer in DNA replication,  In Ribosome- RRNAs are their constituents of ribosome,  Role in genetic code- mRNA contains the codon the carry genetic messages from DNA by transcription which are translated into the language of proteins,  Protein synthesis-All the three type of RNAs take part in the biosynthesis of proteins which are transformed into the protoplasmic structures along with diverse set of enzymes,  Polypeptidyl Processing-It is carried out by small cytoplasmic RNA ( scRNAs),  Ribozyme - a non-protein enzyme is made up of RNAs , Ribonuclease-P and peptidyltransaferase enzymes are also made up of RNAs,  RNA processing- snRNA participate in splicing and processing of RNAs.
  • 38. Nucleic acid chemistry - UV absorption, effect of acid and alkali on nucleic acids.  UV RADIATION is a part of electromagnetic radiation that lies between 200-400 nm, with shorter wavelength between violet and visible spectrum. The range is further sub-divided into short wave (200-280 nm , UV- C),middle wave (280-320, UV-B), and long wave (320-400 nm, UV-A) of light.  UV-C is very dangerous and lethal .It causes the DNA damage via two distinct type of mutations- Dimerizing mutations and Oxidative mutations  In fact, UV-A radiation commonly damages DNA in an oxygen-dependent manner that involves photosensitization. This leads to the production of a free radical that then interacts with and oxidizes DNA bases. These oxidized bases don't pair correctly during replication, resulting in mutations.  One example: G to T transversion mediated by reactive oxygen species (ROS). The oxidation of Guanine into 8-Oxyguanine prevents the hydrogen bonding required to base pair with Cytosine. Instead during replication, 8- Oxyguanine can base pair with Adenine via two hydrogen bonds. When the
  • 39. EFFECT OF UV ON DNA
  • 40. • Strand is synthesized, the base position originally occupied by a Guanine is replaced with a Thiamine , leading to a G to T transversion Oxidative mutation can results in single strand break. • DIMERIZING MUTATIONS: exposure to UV-B and lesser extent of UV-A leads to the formation of common photochemical products in DNA- Cyclobutane pyrimidine dimmers (CPD)as well as Pyrimidine (6- 4)pyrimidone photoproducts(64pps).CPDs formed when two adjacent pyrimidine (thymine, TT or Cytosine, CC) become covalently linked by their C=C bonds. These four carbons form a cyclic ring (Cyclobutane) that links the two pyrimidine, thus creating a chemical intermediate not normally found in DNA.The photochemical product cause a kick in the DNA that prevents the Pyrimidine base pairing and prevents DNA replication. Unlike oxidative mutations, UV induced dimerized mutations arise from the direct absorption of UV photons.
  • 41. EFFECT OF UV ON DNA
  • 42. EFFECT OF pH ON DNA  Nucleic acids are acidic because of the presence of phosphate group along with the proton which is easily lost.  The stability of DNA is governed mainly by the two factors-the two strands double helix along with the base pairing among complementary strands as well as the stacking present in between the neighboring nucleotides.  Non-physiological factors like temperature , pH, ionic strength break the DNA helix and cause conformational change even though the DNA is relatively stable in the aqueous solution.  In a neutral pH range, pH 5 to 9, DNA molecules are quite stable. However, if the pH becomes too acidic or alkaline, DNA molecules are prone to destabilization. At pH 5 or lower, DNA is liable to depurination (i.e. the loss of purine bases from DNA).  DNA is sensitive to alkaline denaturation at high pH at 9.0 because of hydroxides present . These negatively charged ions denature DNA strands by disrupting hydrogen bonds among them.
  • 43. EFFECT OF pH ON DNA
  • 44. EFFECT OF pH ON DNA • Unlike RNA, each sugar group of DNA lacks hydroxyl group at 2' position. Because of the difference, DNA substantially more stable in the alkali solution. • Acidic pH stabilizes crucial intermolecular and intramolecular RNA bonds, including those important for protein synthesis evolution and promotes extra protonated base interactions, allowing RNA to behave under these settings without being bound by traditional base pairing constraints. • So, from the above observation, it is quite clear that the different physical parameters like UV ray, acid, alkali have stron impact upon the stability of the DNA structure. • The different kind of the physical factors like metal ions along with the other parameters are employed to undertake the different experimental procedure in the domain of nucleic acid.
  • 45. OTHER FUNCTIONS OF NUCLEOTIDES – SOURCE OF ENERGY, COMPONENT OF COENZYMES  Nucleotide compounds play significant role in the physiological activities of the living organisms.  ATP plays significant role in energy metabolism. The energy release and absorption in the body is mainly reflected by the production and consumption of ATP.  They provide chemical energy beside in the form of the nucleoside triphosphates, adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP)— throughout the cell for the many cellular functions that demand energy, including: amino acid, protein and cell membrane .  Metabolism of some substances along with adenylate is also acts as a component of some coenzymes like coenzyme I, II and coenzyme A.  Besides, cyclic nucleotides have certain regulatory effect on many basic biological processes.
  • 46. THANKS FOR YOUR HAPPINESS • ACKNOWLEDGEMENT:  Cell and Molecular Biology- Ajoy Paul,  National Institute of Health website,  Khan Academy,  Google for images,  Different web pages for the content,  Different others for directly or indirectly associated with this presentation. • Disclaimer:  This presentation has been developed for the academic fraternity as a part of the enrichment of online study materials without any kind of financial interest. If somebody have the pleasure of happiness, the author will be grateful to far off friends.