1. DNA is composed of nucleotides containing deoxyribose, phosphate groups, and one of four nitrogenous bases (A, T, G, C). 2. RNA is similar in structure but contains ribose rather than deoxyribose and uracil rather than thymine. 3. There are three main types of RNA - rRNA, tRNA, and mRNA - which have different functions like forming ribosomes or carrying genetic code for protein synthesis.

1. Rashmi Vijay

2.  A pentose sugar – deoxy riobose sugar
 Nucleotides – A,T,G,C
 a phosphate

3.  Deoxyribose sugar
 4 C atoms and oxygen molecule forms the ring
 5th C atom is outside the, part of CH2 group
 3 OH groups at positions 1,3,5

4. Purines are double ring compounds with 5 membered imidazole ring joined to
pyrimidine ring at positions 4’ and 5’
Pyrimidines are single ring compounds with nitrogenous bases at positions 1,3 of a 6
membered benzene ring

5.  Alternate with deoxyribose sugars joined by
3’-C atom of one deoxyribose to 5’-C atom of
the other

6.  Nucleotide = a nitrogenous (nitrogen-
containing) base + a pentose + a phosphate
 Nucleoside = a nitrogenous (nitrogen-
containing) base + a pentose

10. Nucleotide Base Pairing

12. Formation of
Phosphodiester bonds
to make a
polynucleotide strand

14.  The discovery of the structure of DNA by Watson
and Crick in 1953 was a momentous event in
science, an event that gave rise to entirely new
disciplines and influenced the course of many
established ones.
 Won Nobel Prize

16. 1. Right handed double helix, wound around central axis with
plectonemic coiling.
2. Two polynucloetide strands run antiparallel
3. The offset pairing of the two strands creates a major groove
and minor groove on the surface of the duplex
4. Phosphate and dRibose forms the back bone of each
polynucloetide strand
5. Nitrogen bases are projected inward
6. Two polynucloetide strands held together by H- bonds , AT
and GC
7. Each base pair tilts 360 and hence has 3600, and each of this
turn has 10 nucleotide base pair
8. Bases are place at a distance of 3.4 A0
9. Diameter of the helix 20 A0
10. Molecular weight / unit length = 2x10 6/ micrometr

19.  To shed more light on the structure
of DNA, Rosalind Franklin and
Maurice Wilkins used the powerful
method of x-ray diffraction to
analyze DNA fibers.
 They showed in the early 1950s that
DNA produces a characteristic x-ray
diffraction pattern.
 In 1953 Watson and Crick postulated
a three dimensional model of DNA
structure that accounted for all the
available data.

21.  Erwin Chargaff developed a chemical
technique to measure the amount of each
base present in DNA.
 Chargaff also observed certain regular
relationships among the molar
concentrations of the different bases.
 These relationships are now called Chargaff’s
rules

22. Chargaff’s rules
 He found that the base composition of the DNA, defined as
the percent G+C, differs among species but is constant in
all cells of an organism and within a species.

23.  The biochemical investigation of DNA began with Friedrich
Miescher, who in the year 1868 isolated a phosphorus-
containing substance, which he called “nuclein,” from the
nuclei of pus cells (leukocytes) obtained from discarded
surgical bandages.
 Miescher and many others suspected this substance is in
some way with cell inheritance, but the first direct evidence
that DNA is the bearer of genetic information came in 1944
through a discovery made by Oswald T. Avery, Colin
MacLeod, and Maclyn McCarty.

24.  These investigators found that DNA
extracted from a virulent (disease-causing)
strain of the bacterium Streptococcus
pneumoniae, also known as pneumococcus,
genetically transformed a nonvirulent strain
of this organism into a virulent form.

25.  When injected into mice, the encapsulated strain of pneumococcus is
lethal, whereas the nonencapsulated strain, like the heat-killed
encapsulated strain, is harmless.
 Earlier research by the bacteriologist Frederick Griffith had shown
that adding heat-killed virulent bacteria (harmless to mice) to a live
nonvirulent strain permanently transformed the latter into lethal,
virulent, encapsulated bacteria.
 Avery and his colleagues extracted the DNA from heat-killed virulent
pneumococci, removing the protein as completely as possible, and
added this DNA to non-virulent bacteria.
 The DNA gained entrance into the non-virulent bacteria, which were
permanently transformed into a virulent strain.
 Avery and his colleagues concluded that the DNA extracted from the
virulent strain carried the inheritable genetic message for virulence.

26.  A second important experiment provided independent
evidence that DNA carries genetic information.
 In 1952 Alfred D. Hershey and Martha Chase used radioactive
phosphorus (32P) and radioactive sulfur (35S) tracers to show
that when the bacterial virus (bacteriophage) T2 infects its
host cell, Escherichia coli, it is the phosphorus-containing
DNA of the viral particle, not the sulfur-containing protein of
the viral coat, that enters the host cell and furnishes the
genetic information for viral replication

28.  DNA is a remarkably flexible molecule.
 Many significant deviations from the Watson-
Crick DNA structure are found in cellular DNA,
some or all of which may play important roles in
DNA metabolism.
 These structural variations generally do not
affect the key properties of DNA defined by
Watson and Crick: strand complementarity,
antiparallel strands, and the requirement for A=T
and G C base pairs.

29.  Structural variation in DNA
reflects three things:
 the different possible
conformations of the deoxyribose,
 rotation about the contiguous
bonds that make up the
phosphodeoxyribose backbone,
and
 Free rotation about the C-1–N-
glycosyl bond

30. Comparison of A, B, and Z forms of DNA.
Each structure shown here has 36 base pairs.
The bases are shown in gray, the
phosphate atoms in yellow, and the riboses
and phosphate oxygens in blue. Blue is the
color used to represent DNA strands in later
chapters.

33.  The Watson-Crick structure is  Whether A-DNA occurs in
also referred to as B-form cells is uncertain, but there is
DNA, or B-DNA, which is evidence for some short
the most stable structure for stretches (tracts) of Z-DNA in
a random-sequence DNA both prokaryotes and
molecule under physiological eukaryotes.
conditions and is therefore
the standard point of  These Z-DNA tracts may play
reference in any study of the a role (as yet undefined) in
properties of DNA. regulating the expression of
some genes or in genetic
 Two structural variants that recombination.
have been well characterized
in crystal structures are the A
and Z forms.

34.  Single stranded polymer of nucleotide monomers made
of Ribose sugar, Nitrogenous bases and Phosphate
group
 The structure of RNA is similar to, but not identical with,
that of DNA.
 There is a difference in the sugar (RNA contains the
sugar ribose instead of deoxyribose), RNA is usually
single-stranded (not a duplex), and
 RNA contains the base uracil (U) instead of thymine (T),
which is present in DNA.

35.  Serves as genetic material in some Viruses
 Present in 3 predominant forms rRNA, tRNA
and mRNA
 Normally doesn't replicate or transcribe
 Made of fewer nucleotides (max 12000)
 Chain starts with adenine or guanine
 Contents expressed in terms of
sedimentation coefficients ‘S’ – Svedberg
constant

36.  rRNA = forms 80% total cellular RNA
 tRNA = 10-20% total cellular RNA
 mRNA = 3-5% total cellular RNA

37.  Found in Ribosomes
 most abundant RNA in cells (75%)
 most stable RNA in cells

38.  four species rRNA in eukaryotes
 28S rRNA (large subunit)
 5.8S rRNA (large subunit)
 5S rRNA (large subunit)
 18S rRNA (small subunit)
 28, 18 & 5.8S rRNA are synthesized as a single transcript, then
processed -DNA has one promoter, one termination sequence for all
three pieces of rRNA -DNA has multiple copies of the whole
transcription unit.
 cut into pieces yielding four spacers & 3 rRNAs.
 spacers are broken down to nucleotides.
 rRNA pieces bind ribosomal proteins and begin to self assemble into
ribosomal subunits
 5S rRNA transcribed from another gene as a separate transcription unit
 three species of rRNA in prokaryotes 23S in large subunit, 5S in the
large subunit and 16S in the small subunit

39. Types of rRNA

40.  Made up of nucleotides twisted around itself at
some region forming helical structure
 The strand assumes a shape of rod, coil or extended
strand depending on ionic strength, temp, pH.
 In helical region, most of the bases are
complementary and are joined by H – bonds
 The unpaired/unfolded single strand will have bases,
and are not complementary, hence don’t show
purine-pyrimidine equality
 rRNA strand unfold upon heating and refold on
cooling

41. Secondary structures of rRNA

42. Secondary structures of rRNA

43.  Jacob and Monod coined the term mRNA
 least abundant (about 5%) of cellular RNAs
 mRNA may be mono or poly cistronic.
 bacterial mRNA is not processed
 eukaryotic mRNA is processed
 initial eukaryotic transcripts are quite large
 allows for posttranscriptional regulation of gene expression
 introns, exons and splicing
(1) eukaryotic mRNAs contain "introns“
(2) introns = intervening sequences
(3) exons = expressed sequences
(4) introns must be excised from mRNA before translation
(5) RNA splicing = process of excising introns from mRNA and splicing the
mRNA back together

45.  Single stranded linear molecule without any
base pairing (base pairing destroys its nature)
 They have complementary sequence to the
segment of DNA on which they are
transcribed

46.  Cap: region at 5’ end. Important for protein synthesis, otherwise mRNA
binds poorly to ribosomes. cap protects mRNA from 5'-endonucleases
 Non coding region - I (leader): region next to cap with 10-100 nucleotides.
Rich in A & U residues and doesn't translate into proteins
 Initiation codon: region next NC-I. Common in both Prokaryotes and
Eukaryotes
 The coding region: consists an average of 1500 nucleotides, which
translates in to amino acids
 Termination Codon: do not code for any amino acids and thus brings
termination of translation
 Non coding region – II (trailer): consists about 50-150 nucleotides. doesn't
translate into proteins. Contains AAUAA in all sequenced examples
 Poly ‘A’ sequence: present at 3’ end. Contains about 200-250 nucleotides,
which become shorter with age of the organism. Poly ‘A’ is added in
nucleus before m-RNA reaches the cytoplasm from nucleus.

47. mRNA has rapid turnover.
 rRNA & tRNA are stable (days, months) -
rRNA deeply buried in structure of ribosomes
 both rRNA and tRNA have many modified
bases -modified bases help protect against
nuclease attack
 mRNA turns over fast
 bacterial mRNA half life = minutes
 eukaryotic mRNA half life = hours

48.  nucleotide composition of mRNA : mRNA base
composition like total genomic DNA
 base sequence complementarity of mRNA:
measure complementarity by doing RNA-DNA
hybridization
 size heterogeneity: mRNA varies greatly in size
relative to rRNA & tRNA. mRNA varies in size
depending on protein for which it codes
 gene amplification: one gene (DNA) gives rise
to many transcripts (mRNA). each transcript can
be translated to many proteins. get more
proteins faster

49.  2nd most abundant (20%) RNA in cells
 synthesized in precursor form and then processed
 16 nucleotide leader sequence removed from 5' end
and terminal UU is removed from 3' end ,UU replaced
by CCA
 CCA found at the 3' end of all functional tRNAs
 intron "loop" is removed
 many bases methylated
 many bases modified –
 uracil converted to dihydrouracil, ribothymine or
pseudouridine
 adenine converted to inosine
 Transfer RNAs vary in length from 73 to 93 nucleotides.

50. Nucleotide sequence of yeast tRNA Ala.
This structure was deduced in 1965 by Robert W.
Holley and his colleagues;
it is shown in the cloverleaf conformation in
which intrastrand base pairing is maximal.
The following symbols are used for the modified
nucleotides (shaded pink): ,
Ψ, pseudouridine;
I, inosine;
T, ribothymidine;
D, 5,6-dihydrouridine;
mI I, 1-methylinosine;
m1G, 1-methylguanosine;
m2G, N2-dimethylguanosine
Blue lines between parallel sections indicate
Watson-Crick base pairs.
The anticodon can recognize three codons for
alanine (GCA, GCU, and GCC).
Note the presence of two G=U base pairs,
signified by a blue dot to indicate non-Watson-Crick
pairing.
In RNAs, guanosine is often basepaired with
uridine, although the G=U pair is not as stable as the
Watson- Crick G=C pair

51. Extra nucleotides occur in the extra arm or in
the D arm.
Two of the arms of a tRNA are critical for its
adaptor function.
The amino acid arm can carry a specific
amino acid esterified by its carboxyl group to
the 2- or 3-hydroxyl group of the amino acid
residue at the 3 end of the tRNA.
The anticodon arm contains the anticodon.
The other major arms are the D arm (DHU
arm), which contains the unusual nucleotide
dihydrouridine (D), and the T Ψ C arm, which
contains ribothymidine (T), not usually present
in RNAs, and pseudouridine (Ψ), which has an
unusual carbon–carbon bond between the base
and ribose.
The D and T Ψ C arms contribute important
interactions for the overall folding of tRNA
molecules,
and the T Ψ C arm interacts with the large-
subunit rRNA.