Franklin collected x-ray diffraction data in the early 1950s that showed DNA has two periodicities: 3.4 Å and 34 Å. Watson and Crick then proposed a 3D model of DNA that accounted for Franklin's data, representing the first model of the DNA double helix structure. This established that DNA is made of two antiparallel strands coiled around each other.

1. DNA structure determination
10/10/0533
• Franklin collected x-ray
diffraction data (early 1950s)
that indicated 2 periodicities
for DNA: 3.4 Å and 34 Å.
• Watson and Crick proposed a
3-D model accounting for the
data.

2. CELL STRUCTURE AND
BIOMOLECULES
Molecular biology- Energy based flow of
information from DNA to RNA to
proteins and enzymes i.e. from Hypo
pituitary access to hormones to
homeostatic etc.

3. The mother of all biomolecules
10/10/05
42
1ffk
Large subunit of the ribosome(proteins at least)

7. Chromatin Structure

8. INACTIVE &ACTIVE CHROMATIN
• Active (transcriptionally active)differ
from from inactive region.
• DNA in active region contain large
regions(100,000bp)prone to digestion by
Dnase- I (single strand cut)

9. MAJOR AND MINOR
GROOVES
• MINOR
– EXPOSES EDGE FROM WHICH C1’ ATOMS
EXTEND
• MAJOR
– EXPOSES OPPOSITE EDGE OF BASE PAIR
• THE PATTERN OF H-BOND POSSIBILITIES IS
MORE SPECIFIC AND MORE
DISCRIMINATING IN THE MAJOR GROOVE

11. DNA structure
10/10/05
34
Fig. 8-15
•DNA consists of two
helical chains wound
around the same axis in
a right-handed fashion
aligned in an antiparallel
fashion.
• There are 10.5 base pairs,
or 36 Å, per turn of the
helix.
• Alternating deoxyribose and
phosphate groups on the
backbone form the outside
of the helix.
• The planar purine and
pyrimidine bases of both
strands are stacked inside
the helix.

13. Much of Genome is not
TRANSCRIBED
• The entire human haploid
genome contain sufficent DNA to
code for app. 1.5 million genes.
• Human genome encodes less
than 100,000 proteins ie 1% of
human genome.
• 24% of genome as Introns

14. More than half DNA of Eukaryotic is
non Repetitive Sequences.
• In humans 10,000 to 15000 . genes are
expressed.
• Different combination of genes are
expressed in each tissue,of course and
how this is accomplished in one of the
major unanswered question in biology.

15. 30% of Human Genome has
Repetitive sequences
• A.Highly repetitive: 5-500 bp length
repeated many times.(these seq. are
transcriptionaly inactive)may play role in
structure of ch.
• B. Moderately repetitive: 106
copies
per haploid genome are not clustered but
are interspred with unique seq.
• C. Microsatelite repeat seqs.2-6bp
repeated up to 50 times(AC=TG)AC
repeat seqs. Are50000-100000 locations
in genome.

16. TELOMERE
• The ends of each chromosome
contains structures called TELOMERES
• Telomere consist of short repeat TG
sequences.(5’-TTAGGG-3’)can run for
kb.
• TELOMERASE ( RNA+RNA dependent
DNA polymerasesor{ Reverse
transcriptase} is responsible for
telomere synthesis) & maintains length
of telomere.

17. Cont………………………….
• Genome of Prokaryotes are
circular.human &Eukaryotes is linear as
result the lagging strand has incomplete
51 end. Each round of replication would
shorten the chromosome.Telo=End.
• How are repeated sequences generated
the enzyme TELOMERASE performs this
function.
• The protein component of
telomerases,hence it acts as reverse
transcriptase.that carries its own template.
• Telomerase levels are raised in cancer
cells.

18. DNA
• Two helical polynucleotide chains
are coiled around a common axis.
• The chains run in opposite
directions.(Template and Coding)
• Sugar-Phosphate backbones are
on the outer side and Purine
&Pyrimidene bases lie on the
inside of helix.
• The bases are prepandicular to the
helix axis. (10 bases per turn of
Helix)
• Diameter of helix is 20 Ao.

19. Cont………………………..
• In between large regions there
are shorter streches (100-
300)which are more sensative
to Dnase-I These sites provides
a sight for transcription.
(euchromatin)
• Transcriptionally inactive ch. Is
densly packed.
(Hetrochromatin)

20. A-DNA
• RIGHT-HANDED HELIX
• WIDER AND FLATTER THAN B-DNA
• 11.6 BP PER TURN
• PITCH OF 34 A
  AN AXIAL HOLE
• BASE PLANES ARE TILTED 20 DEGREES
WITH RESPECT TO HELICAL AXIS
– HELIX AXIS PASSES “ABOVE” MAJOR GROOVE
  DEEP MAJOR AND SHALLOW MINOR
GROOVE
• OBSERVED UNDER DEHYDRATING
CONDITIONS

21. B-DNA
• B-DNA Right handed double helix.
• Supercoils store energy.
• Supercoiled DNA is prefered form.
• DNA of E.coli is1.4mm, 4.7million
bp.
• Eukaryotes contain more than ten
times of DNA as compaired to
prok.

22. Z-DNA
• A LEFT-HANDED HELIX
• SEEN IN CONDITIONS OF HIGH SALT
CONCENTRATIONS
– REDUCES REPULSIONS BETWEEN CLOSEST
PHOSPHATE GROUPS ON OPPOSITE
STRANDS (8 A VS 12 A IN B-DNA)
• IN COMPLEMENTARY POLYNUCLEOTIDES WITH
ALTERNATING PURINES AND PYRIMIDINES
– POLY d(GC) · POLY d(GC)
– POLY d(AC) ⋅ POLY d(GT)
• MIGHT ALSO BE SEEN IN DNA SEGMENTS WITH
ABOVE CHARACTERISTICS

23. B,A and Z DNA
10/10/0538
Fig. 8-19
• B form - The most common
conformation for DNA.
• A form - common for RNA
because of different sugar
pucker. Deeper minor groove,
shallow major groove
• A form is favored in conditions
of low water.
• Z form - narrow, deep minor
groove. Major groove hardly
existent. Can form for some
DNA sequences; requires
alternating syn and anti base
configurations.
36 base pairs
Backbone - blue;
Bases- gray

24. DNA strands
10/10/05
37
Fig. 8-16
• The antiparallel strands of DNA
are not identical, but are
complementary.
• This means that they are
positioned to align complementary
base pairs: C with G, and A with
T.
• So you can predict the sequence
of one strand given the sequence
of its complement.
• Useful for information storage
and transfer!
• Note sequence conventionally is
given from the 5' to 3' end

25. Discovering the structure of DNA
• DNA = Deoxyribose nucleic acid
• Made out of sugars (deoxyribose), phosphates
and nitrogen bases

26. Difference between
DNA and RNA
• Sugar: DNA;deoxyribose.
• RNA; Ribose.
• DNA: A,T,G,C.: RNA;A,U,G,C.
• DNA Double,RNA single stranded.
• DNA A=T,G=C, RNA; U=A,,G=C not.
• RNA can be hydrolysed by
Alkali,DNA not.

27. HISTONES:
• H1
• H2A
• H2B
• H3
• H4
Acetylation linked with replication,H1
with condensation,DNA
repair,transcription
repression,methylation of histones
activation and repression of gene.

30. HISTONES
• Most abundant basic chr.protein.
• H1Loosly bound to chr,&not not
necessary,but adjecent nucleosome
is joined by H1, nucleosome
• Nucleosome contain four types of
histones.H2A,H2B,H3 and H4
• Function identical in all eukaryotes.
• Four core Histones are subject to 6
types of covalent modifications

31. HISTONES
• Acetylation,Methylation,Phosphory
lation,ADP-
ribosylation,monoubiquitylation
and Sumoylation.
• H3,H4 form tetramer
• h2A &H2B form Dimer.Under
physiologic conditions
olig.associate & form octamer.
• The amino tail(His) is available co-
valent modifications
• One octamer has 1.75 turns of DNA
(146bp)

32. The mother of all biomolecules
10/10/05
42
1ffk
Large subunit of the ribosome(proteins at least)

33. Z-DNA
• 12 (W-C) BASE PAIRS PER TURN
• A PITCH OF 44 DEGREES
• A DEEP MINOR GROOVE
• NO DISCERNIBLE MAJOR GROOVE
• REVERSIBLE CHANGE FROM B-DNA TO
Z-DNA IN LOCALIZED REGIONS MAY ACT
AS A “SWITCH” TO REGULATE GENE
EXPRESSION
– ? TRANSIENT FORMATION BEHIND
ACTIVELY TRAN-
SCRIBING RNA POLYMERASE

34. FORCES THAT STABILIZE
NUCLEIC ACID STRUCTURES
• SUGAR-PHOSPHATE CHAIN
CONFORMATIONS
• BASE PAIRING
• BASE-STACKING,HYDROPHOBIC
• IONIC INTERACTIONS

35. DNA TOPOLOGY
• THE TOPOLOGICAL PROPERTIES OF DNA HELP US
TO EXPLAIN
• DNA COMPACTING IN THE NUCLEUS
• UNWINDING OF DNA AT THE REPLICATION FORK
• FORMATION AND MAINTENANCE OF THE
TRANSCRIPTION BUBBLE
• MANAGING THE SUPERCOILING IN THE
ADVANCING TRANSCRIPTION BUBBLE

39. mRNA (messenger RNA)
• mRNA is synthasized from DNA by
enzyme RNA Polymerase.
• Introns and Exons.(Hetrogenous
hnRNA)
• Most hetrogenous,highly elongated
and short lived.
• Has 5’—3’ polarity complimentary to
coding strand.
• For protein synthesis.
• Stable in Euk. Unstable in Pro.

43. tRNA (Transfer RNA)
• Much smaller in size (75-90
ribonucleotide)Clover leaf shaped.
• 15% of total cellular RNA.
• 20 species of tRNA.
• It acts as adaptor molecule.
• 40 different tRNA.
• Five arms of tRNA: 1:D-Arm; 2:TUC-
Arm 3: CCA Arm(Acceptor) 4:
Anticodon Arm 5: Variable Arm or
Extra Arm (determine Sp.).

44. tRNA
• Amino Acid acceptor arm 7 base pair
stem
• 5’—3’ CCA.Links Amino Acid.AA are
linked co-valently to corresponding
tRNA by enz.AAtRNA Synthetase.
• Anticodon Arm Has 5-bp loop and
triplet nucleotide
sequence(anticodon) complimentary
to codon.
• DHU arm .3-4 base pairs.
• TUC arm stem has 5 bp.

45. RIBOSOMAL RNA
• Are present in Ribosomes in
association with many polypeptides.
• 80 % of total cellular RNA.
• Very complex in Euc. Two sub-units
(60S)and (40S)
• Protein Synthesis.
• Larger unit has 3 RNA ie 5S,5.8S,28S
with 50 polypeptides.
• Smaller subunit has 18S and 30
polypeptides.

50. MITOCHONDRIAL DNA
• 54 out of 67 genes are coded by
nuclear genes,rest are coded by
Mitochondria.(mt)
• It form 1% of total cellular DNA.
• It codes 13 proteins that play key role
in the respiratory chain.

51. Features of mtDNA
• Circular,double stranded
• Contains 16,569 bp
• Encodes 13 protein subunits.
• Encodes 22 mt. tRNA molecules.
• Encodes(16s) and a small (12s)mt rRNA
• Very few untranslated sequences.
• High mutation rate (5-10 times to nucl.)
• M for M (Maternaly inherited Mitochondria)

52. Discovering the structure of DNA
• DNA = Deoxyribose nucleic acid
• Made out of sugars (deoxyribose), phosphates
and nitrogen bases

53. The mother of all biomolecules
10/10/05
42
1ffk
Large subunit of the ribosome(proteins at least)

54. • Mitochondria
Function- ATP synthase, fatty acid oxidation, Krebs cycle, cytosolic
Ca2+
regulation.
Marker- Succinate dehydrogenase, glutamate dehydrogenase.

58. Redox potential of some redox system
Redox system Eo`(volt)
NADH/NAD+
-0.32
Succinate/Fumarate -0.32
FADH2/FAD 0.0
Coenzyme Q.H2/CoQ 0.10
Cytochrome b (Fe2+
/Fe 3+
) 0.12
Cytochrome c1 (Fe2+
/Fe 3+
) 0.22
Cytochrome a (Fe2+
/Fe 3+
) 0.29
Cytochrome a3 (Fe2+
/Fe 3+
) 0.39
HO2/1/2
O2 0.82

60. • Endoplasm reticulum (2 type RER & SER)
Function- Production of excretory proteins, glycosylation, drug
metabolism.
Marker- Glucose-6-phosphatase.
• Golgi complex
Function- Synthesis of lipoprotein, formation of lysosomes, secretion
of proteins.
Marker- Galactosyle transferase, Fucosyle transferase.
• Peroxisomes
Function- Fatty acid oxidation, detoxification of H2O2.
Marker- Catalase, uric acid oxidase.

61. • Lysosomes
Function- Intracellular digestion and detoxification.
Marker- Acid phosphatase.