Slide 1 : THE GENETIC MATERIAL
:DNA : STRUCTURE
PART-II
DNA STRUCTURE
11-8-2011 5.30 PM
BY
Dr. Ichha Purak
http://www.dripurak.com/
http://drichhapurak.webnode.com/ PART OF DNA DOUBLE HELIX
Discovery of DNA : Discovery of DNA Friedrick Miescher (1869) , a Swiss chemist first identified nuclein from nuclei of human white blood cells which was later on renamed as Nucleic acid . It was rich in phosphorus having no sulphur so was different than protein.
From
Slide 3 : Russian Biochemist Phobebus Levene (1910) is credited to discover Phosphate-Sugar-Base as three components of Nucleotide . He also mentioned DNA as polynucleotide (Any one of four adenine,Cytocine,Thymine /Guanine ).He also stated difference between Ribose and Deoxyribose Sugar
Slide 4 : POLYNUCLEOTIDE
HISTORY OF DNA : HISTORY OF DNA William Astbury (1938) detected a periodicity of 3.4 angstroms
Rosalind Franklin (1952) performed - X- ray diffraction analysis of DNA crystal
Franklin and Wilkins (1950-1953) confirmed 3.4 periodicity and noted uniform diameter of 20A○ (2nm)
Watson and Crick (1953 ) proposed the DNA double helical model based on Franklin’s X-ray crystallography Analysis and other evidences
Slide 6 : 1962: Nobel Prize in Physiology and Medicine James D.
Watson Francis H.
Crick Maurice H. F.
Wilkins Rosalind Franklin
Slide 7 : X-ray Crystallography of DNA by Franklin and Wilkins
(1950-52 showing helical symmetry
Slide 8 : DNA is one of the two nucleic acids ( RNA and DNA )
DNA is long, unbranched and spirally coiled in Eukaryotes and circular in prokaryotes as well as mitochondria and plastids
In Prokayotes DNA is present only in Nucleoid and is Monocistronic, but in Eukaryotes DNA is present in Nucleus, Mitochondria and Plastids and is Polycistronic.
DNA is genetic material ,carries heredity characters over generations through DNA Replication ( DNA DNA )and Transcription ( DNA RNA ) followed by Translation
Slide 9 : Nucleic Acids are fibre like molecules ( Length is many times the breadth )
Nucleic Acids are polymers of Nucleotides. DNA is a macromolecule of high Molecular Weight
Nucleotides consists of sugar, Phosphoric Acid and bases ( Purine /Pyrimidine)
J D Watson and Francis Crick (1953 ) have proposed a double helical structure (Model) of DNA , for which they have received the Nobel Prize of 1962.
Slide 10 : According to this Model some facts about DNA are as follows :
DNA has a double helical structure made by twisting around of 2 very long thin polymeric strands around a common (imaginary) axis.
Slide 11 : The original DNA model by Watson and Crick. Photo: Cold Spring Harbor Laboratory Archives Imaginary axis is shown by a line passing through the centre longitudinally
DNA Double Helix : DNA Double Helix
Slide 13 : Two strands are antiparallel, complementary
in sequence of bases and are joined by
Hydrogen (H) bonds
Slide 14 : Each strand is polymer of deoxy ribonucleotides. 1 2 3 4 5 6
Slide 15 : Each Deoxyribonucleotide is made up of a Deoxyribose sugar, a phosphate, a Nitrogenous Base, which may be either a Purine or Pyrimidine
Deoxy ribose sugar has formula C5 H10 O4 and is derived from Ribose sugar C5H10O5 by loss of one oxygen atom at C-2 position
Phosphate (PO4) is derived from Phosphoric acid (H3PO4)
Slide 16 : Figure : Nucleotides have three components.
A nucleotide consists of a phosphate group, a pentose sugar (ribose or deoxyribose), and a nitrogen-containing base, all linked together by covalent bonds. The nitrogenous bases have two different chemical forms: purines have two fused rings, and the smaller pyrimidines have a single ring.
© 2008 by Sinauer Associates, Inc. All rights reserved. Used with permission.
Slide 17 : 17 Deoxyribose – C5 H10 O4
Ribose- C5H10O5 Adenine-6-amino Purine
Guanine- 2-amino 6 oxy Purine
Cytocine- 6- amino pyrimidine
Thymine- 5- methyl 6 oxy pyrimidine
Uracil- 6-oxy pyrimidine
Slide 18 : Nitrogenous Base are either Pyrimidine -6 membered ring (Basic Skeleton 4C-2N ) and Purine- two rings (Basic Skeleton 5C-4N ) . Cytosine ( C ) and ( T ) are pyrimidines of DNA and Adenine ( A ) and Guanine (G ) are the Purines of DNA
In a deoxyribonucleotide phosphate is attached at C-3 or C-5 of deoxy ribose sugar and base is attached to C-1 of sugar
A) Sugar+ Base forms Nucleoside ( S-B )
B) Sugar + Base + Phosphate forms Nucleotide
( P-S-B )
Slide 19 :
Slide 20 : Sugar and Phosphate of the nucleotides are linked together forming exterior of frame work of the strands.
PO4 are linked between two sugar molecules at C3 & C5 position by formation of Phosphodiester bonds. PO4 are exposed to exterior as they are ( - ) vely charged and are hydrophilic.
Slide 21 :
Slide 22 : In DNA deoxyribo nucleotides are held together by phosphodiester bonds.
Slide 23 : What chemical forces hold the two DNA strands together?
Slide 24 : Two strands are connected to each other by means of base pairing which comprise the steps of the ladder. Base pairing takes place between one purine and one pyrimidine by H bonds. Although H bonds are weak but many H bonds give stability to the double helical structure.
Slide 25 : The two strands of DNA are oriented in opposite directions. One strand runs in 3’-5’ direction and the other in 5’-3’ direction. This antiparallel orientation also supports the double helical nature of DNA molecule.
There lies close similarity of measurements of AT and GC pairs, distance of A-T is about 1.11 nm and that of G-C is 1.08nm. The angle between C-1 of deoxyribose sugar and N of base is about 51°.
Base Pairing : Base Pairing Hydrogen bonds
Individually weak electrostatic bonds but collectively become strong and provide stability to double helix
Hydrogen bonds between bases : Hydrogen bonds between bases Also important that the purine-pyrimidine base pairs are of similar size.
Slide 28 :
Slide 29 :
Slide 30 : DNA strands also held together by base stacking:
Van der Waals interactions with neighboring base pairs
The evidence for this opinion is based on interference by urea and foramide ,are unable to separate double strand themselves but require heat in addition
Double stranded helix structure is also promoted by having phosphates on outside ,interact with water and K+ and Mg+ +ions
Slide 31 : 31
Slide 32 : Bases are projected inwards and lie perpendicular
to the long sugar & phosphate chains.
Bases are attached to C -1 of sugar and for
attachment N at 3 position of pyrimidine and N at 9
position of Purine is used.
During base pairing Adenine always pairs with
Thymine by 2 H bonds and Guanine pairs with
Cytosine b y 3 H bonds.
A=T G Ξ C
Slide 33 :
Slide 34 : Diameter of double helical structure is constant because of strict pyrimidine (small ) and Purine (large ) base pairing. Diameter of B- DNA is 20 A ° (2 nm)
For one complete turn 34 A° space is required and 10 bp (base pairs ) are present in each complete turn. Each base pair lies at an angle of 36 ° from next base pair
Two strands of DNA run in antiparallel direction. One in 3’ 5’ direction and other in 5’ 3’ direction. The direction depends on attachment of first PO4 group to C3 or C5 of deoxyribose sugar.
Slide 35 : Two strands are coiled around a common axis in such a way ( like a rope ) that deep (major ) and shallow (Minor) grooves are resulted. Proteins can bind with DNA at these locations. Major grooves are 22A° and Minor grooves are 12 A°
Slide 36 :
Slide 37 : Two strands are coiled around each other in such a way that they can not be separated unless ends are permitted to revolve ( just like a rope ) Such coiling is known as Plectonic coiling.
Due to strict base pairing rules , two strands are
complementary to each other in sequence of
bases. This feature helps in determining heredity
through DNA Replication and Transcription.
DNA code consists of only 4 symbols A T G C
Slide 38 : Erwin Chargaff (1949-1953) Digested many DNAs and subjected products to chromatographic separation RESULTS
The sum of Purines is equal to sum of Pyrimidines
A = T, C = G , A + G = C + T (purine = pyrimidine)
but A+T ≠ G +C ( Not equal )
Base ratio A + T/ G+C varies from one species to other and is not always equal to one but is constant for a species.
Chargaff’s Rule : Chargaff’s Rule Adenine must pair with Thymine
Guanine must pair with Cytosine
The amount of Adenine must be equal to amount of Thymine and amount of Guanine must be equal to Cytosine in a given DNA molecule
Slide 40 : Figure : Chargaff's rule.
In DNA, the total abundance of purines is equal to the total abundance of pyrimidines.
© 2008 by Sinauer Associates, Inc. All rights reserved. Used with permission
Slide 41 : DNA with high percentage of G ≡ C pairing
( Mitochondrial DNA ) have more density than those with high A = T pairing. (Nuclear DNA )
Upon heating upto 80-90 º C or more 2 strands of DNA uncoil and separate
( DNA Denaturation ). On cooling the strands come closer and are held together ( DNA Renaturation or Annealing ) This property is used in PCR ( Polymerase Chain Reaction)
Slide 42 : DNA is generally double stranded, but is single
stranded exceptionally in some Viruses viz.
ȹ- 174 & S-13
Both strands of DNA are right handed spirals
except Z DNA ( Left handed spiral )
Alternative Forms of DNA
DNA can exist in several conformational isomers
B form is the “normal” conformation
A form is found in high salt conc
Z form Left-handed helix and 12 bp/turn (Z for
zigzag)
Slide 43 : DNAs are of various types A B C D E & Z , of which B DNA is the most common form . The different types of DNA differ in number of base pairs per turn, pitch, angle, diameter of Helix and handed ness etc. TYPES OF DNA
Slide 44 : A
11 B
10 Z
12 Residues/Turn Clock -wiseTurn Anti Clock-wise Turn
Slide 45 : Figure : DNA can assume several different secondary structures.
These structures depend on the base sequence of the DNA and the conditions under which it is placed. Used with permission. © 2005 by W. H. Freeman and Company. All rights reserved
Right vs. Left Handed Helices : Right vs. Left Handed Helices B Z
Slide 47 : DFFERENCES BETWEEN DNA AND RNA
Slide 48 :
Slide 49 :
Slide 50 : Ribose replaces deoxyribose; uracil replaces thymine RNA
Nucleosides and Nucleotides : Nucleosides and Nucleotides
Slide 52 : SUMMARY OF THE CLASS DNA STRUCTURE DNA ( De oxy Ribo Nucleic Acid ) is one of the two
Nucleic Acid
The Repeating Units of DNA are De-oxy Ribonucleotides
Each Deoxy Ribonucleotide has 3 components Deoxy
Ribose Sugar, Phosphate and Any one N Base ( A/G/T/C)
DNA is double helical in Nature , two strands are coiled
around a common imaginary axis
Slide 53 : Amount of Purines is always equal to amount of Pyrimidines(Charguff’s Rule)
Double helical structure is like a ladder having steps made by base pairs which are projected inwards
Successive De oxy ribonucleotides are linked with each other by Phospho diester bond which is formed by linkage of phosphate with two OH groups of two sugar residues
Slide 54 : Adenine always pairs with Thymine by two Hydrogen bonds and Guanine alwalys pairs with Cytosine by three Hydrogen bonds
Two strands run in opposite directions.
Two strands are complementary to each other in sequence of bases because of strict base pairing rules , A=T, G Ξ C. This feature helps in maintaining the diameter of double helix constant ( Pyrimidine→Purine Pairing) and also making DNA as Genetic Material through Replication and Transcription.
Slide 55 : There are different forms of DNA as B,A ,D,E &Z which differ in No of bp/turn, angle and handedness
DNA differs from RNA in having
Deoxyribose Sugar
Thymine as Pyrimidine
Double stranded helix
B-form of Helix Geometry
Slide 56 : DNA with high percentage of G ≡ C pairing( Mitochondrial DNA ) have more density than those with high A = T pairing. (Nuclear DNA )
DNA may have millions of Nucleotides .Human chromosome number 1 has 220 million base pairs
Slide 57 : THANK YOU
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