structure of dna and rna by shirohi

Structure of DNA and RNA

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NAME : SHIROHI GOVIL ROLL NO : 36 SUBJECT : MOLECULAR

BIOLOGY SEMESTER : III YEAR : 2013-2014 ASSIGNMENT : STRUCTURE OF DNA

AND RNA

STRUCTURE OF DNA AND RNA


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CONTENTS

A. STRUCTURE OF DNA

HISTORIC PERSPECTIVE - discovery of nuclein - scientist summary - derivation of structureDNA STRUCTURE - polymer of nucleotides - formation of polynucleotides - double helixFEATURES OF DOUBLE HELIXTYPES OF DNADENATURATION AND RENATURATIONSTABILITY OF DNA

B. DNA TOPOLOGY LINKING NUMBER TOPOISOMERASES - types of topoisomerases

c. STRUCTURE OF RNA COMPARISON WITH DNA FUNCTIONS - role as enzymes

D. ORGANELLE DNA MITOCHONDRIA DNA CHLOROPLAST DNA


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STRUCTURE OF DNA


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HISTORIC PERSPECTIVE:DISCOVERY OF NUCLEIN

Who discovered DNA?

DNA was isolated, analyzed and recognized as a unique macromolecule in 1869 by Friedrich Miescher, an eminent physiological

chemist from Basel, Switzerland.


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HISTORIC PERSPECTIVE:SCIENTIST SUMMARY

NO.

NAME OF SCIENTIST

CONTRIBUTION TO MOLECULAR BIOLOGY

1 Fredrich Miescher Discovered DNA, named it nuclein.

2 Frederick Griffith Principle of Transformation

3 Joachim Hammerling

Demonstrated significance of nucleus in regrowth, and cell direction.

4 Erwin Chargaff Demonstrated nitrogenous base ratio, and relationship (A-T,G-C).

5 Alfred Hershey and Martha Chase

Demonstrated DNA's role in reproduction and disproved protein's role.

6 Rosalind Franklin Contributed to knowledge of DNA structure.

7 James Watson and Francis Crick

Derived DNA structure with previous scientific knowledge.


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HISTORIC PERSPECTIVE:DERIVATION OF STRUCTURE

In 1948, Linus Pauling discovered that many proteins take the shape of an alpha helix, spiraled like a spring coil.

In 1950, biochemist Erwin Chargaff found that the arrangement of nitrogen bases in DNA always occurred in a one-to-one ratio.

In 1953, James D. Watson and Frances

H.C. Crick determined the double-helix structure of DNA, the molecule containing human genes.


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DNA STRUCTURE:POLYMER OF NUCLEOTIDES

DNA is made of chemical building blocks called nucleotides. These building blocks are made of three parts: a phosphate group, a sugar

group and one of four types of nitrogen bases. There are 2 types of nitrogen bases: purines and pyrimidines. The pyrimidine bases have a 6‐membered ring with two nitrogens and four

carbons. The purine bases have a 9‐membered double‐ring system with four nitrogens and five carbons.


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DNA STRUCTURE:FORMATION OF POLYNUCLEOTIDES

STRUCTURE OF A NUCLEOTIDE FORMING A NUCLEOTIDE CHAIN

Nucleoside is formed when a base is joined to 2’deoxyribose by the removal of a molecule of water between the hydroxyl on the 1’ carbon of the sugar and the base to form a glycosidic bond.

Nucleotide is formed by linking the phosphate to 2’-deoxyribose by removing a water molecule from between the phosphate and the hydroxyl on the 5’- carbon to make a 5’-phosphomonoester.

Nucleotides are joined to each other in polynucleotide chains through the 3’ hydroxyl of 2’-deoxyribose of one nucleotide and the phosphate attached to the 5’ hydroxyl of another nucleotide resulting in a phosphodiester linkage.


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DNA STRUCTURE:THE DOUBLE HELIX


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FEATURES OF DOUBLE HELIX

It contains two polynucleotide strands wound around each other. The backbone of each consists of alternating deoxyribose and phosphate groups. The phosphate group bonded to the 5' carbon atom of one deoxyribose is covalently bonded to the 3' carbon of the next.

The two strands are "antiparallel"; that is, one strand runs 5′ to 3′ while the other runs 3′ to 5′.

The DNA strands are assembled in the 5′ to 3′ direction .

The bases attached to each deoxyribose projects inwards.

Each base forms hydrogen bonds with the one directly opposite it, forming base pairs. 3.4 Å separate the planes in which adjacent base pairs are located. The diameter of the helix is 20 Å.

The double helix makes a complete turn in just over 10 nucleotide pairs.

The helix can be virtually any length; when fully stretched, some DNA molecules are as much as 5 cm (2 inches!) long.

The path taken by the two backbones forms a major (wider) groove and a minor (narrower) groove .


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TYPES OF DNAA- DNA B- DNA

It has 11 base pairs per turn. It is observed under conditions of low

humidity Its major groove is narrower and much

deeper than that of the B form and minor groove is broader and shallower.

DNA does adopt the A structure in certain DNA-protein complexes.

It is observed at high humidity. It has 10 base pairs per turn. It has a wide major groove and a

narrow minor groove. majority of the DNA in the cell is in

the B-form.


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DENATURATION AND RENATURATION

The complementary strands of double helix can also be made to come apart when a solution of DNA is heated above physiological temperatures (to near 100 °C) or under conditions of high pH, a process known as DENATURATION.

When heated solutions of denatured DNA are slowly cooled, single strands often meet their complementary strands and reform regular double helices, a process known as RENATURATION.

the ability to form hybrids between two single-stranded nucleic acids (hybridisation) is the basis for several indispensable techniques in molecular biology, such as Southern blot hybridization and DNA microarrays.

When the temperature of a solution of DNA is raised to near the boiling point of water, the optical density (absorbance) at 260 nm markedly increases.

Reason is that duplex DNA is hypochromic; it absorbs less ultraviolet light by about 40% than do individual DNA chains. The hypochromicity is due to base stacking, which diminishes the capacity of the bases in duplex DNA to absorb ultraviolet light.

Plotting the optical density of DNA as a function of temperature, we observe that the increase in absorption occurs abruptly over a relatively narrow temperature range. The midpoint of this transition is the melting point or Tm.


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STABILITY OF DNA

The melting temperature of DNA is characteristic of each DNA. It is determined by:

a) G:C content of the DNA- G:C base pairs contribute more to the stability of DNA than do A:T base pairs because of the greater number of hydrogen bonds . The higher the percent of G:C base pairs in the DNA , the higher the melting point.

b) Ionic strength of the solution- At high ionic strength, the negative charges of phosphate groups on the strands are shielded by cations, thereby stabilizing the helix.

c) Extremes of pH - these alter the ionization states of the groups on the bases which provide and accept the H-bonds.

d) Interaction with DNA Binding Proteins - some proteins need to transiently open the helix to gain access to the bases within. This is necessary for DNA synthesis (replication) and RNA synthesis.


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DNA TOPOLOGY


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DNA TOPOLOGY: LINKING NUMBER

The total number of times one strand of the DNA helix is linked with the other in a covalently closed circular molecule is known as the linking number , Lk.

1. The linking number is only defined for covalently closed DNA and its value is fixed as long as the molecule remains covalently closed.

2. Lk is always an integer since two strands must always be wound about each other an integral number of times upon closure. The linking number of a covalently closed circular DNA can be resolved into two components called the twists Tw and the writhe Wr . Lk = Tw + Wr

The twists Tw are the number of times that the two strands are twisted abouteach other while the writhes Wr is the number of times that the DNA helix is coiledabout itself in three-dimensional space.

3. Writhe can take two forms : one is interwound or plectonemic writhe, in which the long axis is twisted around itself , and the other is a toroid or spiral in the long axis is wound in a cylindrical manner.

4. Writhing number (Wr) is the total number of interwound and/or spiral writhes in cccDNA (covalently closed , circular DNA).

5. Lk0is the linking number of fully relaxed cccDNA under physiological conditions.

6. DNA in cell is negatively supercoiled. Extent of supercoiling is measured by “linking difference “ΔLk = Lk -Lk0.

-Lk < Lk0 and ΔLk < 0: negatively supercoiled -Lk > Lk0 and ΔLk > 0: positively supercoiled

7. superhelical density ,σ= ΔLk/ Lk0


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DNA TOPOLOGY:TOPOISOMERASES

Topoisomerase(two types): introduce transient single-or double strand breaks into DNA.

Type I Topoisomerases- cut one strand of the double helix, pass the other strand through, then rejoin the cut ends

Type II Topoisomerases- cut both strands of the double helix, pass a region of the duplex between the cut ends, then rejoin the ends.


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DNA TOPOLOGY:TOPOISOMERASES

Topoisomerases can catenate and decatenate circular DNA molecules.

Topoisomerases use a covalent protein – DNA linkage to cleave and rejoin DNA strands.

They form enzyme bridges and pass DNA segments through each other.

DNA topoisomer scan be separated by electrophoresis.

Ethidium ions cause DNA to unwind.


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STRUCTURE OF RNA


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PRIMARY STRUCTURE OF RNA RNA is a polymer of nucleotides linked by phosphodiester bonds. A nucleotide consists of – ribose sugar, phosphate group and nitrogenous base. Base is linked at the 1’ carbon of sugar to form glycosidic bond. Phosphate is linked on 5’ carbon to form 5’ phosphomonoester bond.


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COMPARATIVE ACCOUNT :DNA AND RNA

DNA RNA

Function Medium of long-term storage and transmission of genetic information

Transfer the genetic code needed for the creation of proteins from the nucleus to the ribosome

Predominant structure

Double- stranded molecule

A single-stranded molecule

Bases A, T, C, G A, U, C, G

Sugar 2’- deoxyribose ribose

Stability Deoxyribose sugar in DNA is less reactive because of C-H bonds. Stable in alkaline conditions. DNA has smaller grooves, which makes it harder for enzymes to "attack" DNA.

Ribose sugar is more reactive because of C-OH (hydroxyl) bonds. Not stable in alkaline conditions. RNA has larger grooves, which makes it easier to be attacked by enzymes

Propagation DNA is self-replicating.

RNA is synthesized from DNA when needed


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FUNCTIONS OF RNA:

Intermediate molecule: mRNA Adaptor molecule: tRNA Structural molecule: rRNA Regulatory molecule: Translation of mRNAs Biological catalyst: Enzyme Research: Novel RNA species


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FOLDING OF RNA CHAIN Stem loop structures: RNA chains fold back on

themselves to form base-paired segments between short stretches of complementary sequences. RNA may adopt one of various stem-loop structures in which the intervening RNA is looped out from the end of the double-helical segment as in a hairpin, a bulge, or a simple loop.

Tetraloop: a stem-loop with the “tetraloop” sequence UUCG is stable due to base-stacking interactions in the loop .

Pseudoknot: Base pairing can take place between sequences that are not contiguous to form complex structures named pseudoknots.

G:U base pair: Due to these additional, non-Watson-Crick base pair, RNA chains have an enhanced capacity for self-complementarity. Thus, RNA frequently exhibits local regions of base pairing but not the long-range, regular helicity of DNA.


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RNA ADOPTS COMPLEX TERTIARY STRUCTURES

1. RNA has enormous rotational freedom in the backbone of its non-base-paired regions.2. RNA can fold up into complex tertiary structures frequently involving unconventional base pairing, such as the base triples and base-backbone interactions seen in tRNAs , for example, the U:A:U base pair.3. Proteins can assist the formation of tertiary structures by large RNA molecules, such as those found in theribosome.4. Proteins shield the negative charges of backbone phosphates whose electrostatic repulsive forces would otherwise destabilize the structure.


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RNA AS ENZYMES

RNA enzymes are known as ribozymes, and they exhibit many of the features of a classical enzyme, such as an active site, a binding site for a substrate and a binding site for a cofactor, such as a metal ion.One of the first ribozymes to be discovered was RNase P, a ribonuclease involved in generating tRNA molecules from larger, precursor RNAs. RNase P is composed of both RNA and protein; however, the RNA moiety alone is the catalyst.Other ribozymes carry out trans-esterification reactions involved in the removal of intervening sequences known as introns from precursors to certain mRNAs, tRNAs, and ribosomal RNAs in a process known as RNA splicing.The hammerhead is a sequence-specific ribonuclease that is found in certain infectious RNA agents of plants known as viroids, which depend on self-cleavage to propagate. A self-cleaving sequence , hammerhead is called so because of the shape of its secondary structure, which consists of three base-paired stems (I, II, and III) surrounding a core ofnon-complementary nucleotides required for catalysis ,The tertiary structure of the ribozyme, looks like a wishbone.


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ORGANELLE DNA


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ORGANELLE DNA

A. MITOCHONDRIAL DNA B. CHLOROPLAST DNA - The DNA inside the mitochondrion is

circular in structure and double-stranded.

- Mitochondrial DNA (mtDNA) codes for 13 polypeptides required for oxidative phosphorylation, 22 transfer RNAs, and 2 ribosomal RNAs.

- The heavy strand is purine-rich and the light strand is pyrimidine rich.

- chloroplast also contain circular double stranded DNA molecules.

- They too do not associate with histones. - Chloroplast genome contain two

inverted repeats called IRA and IRB, therefore many genes encoded by chloroplast genome have two copies.

-Both transcription and translation procedure is similar to prokaryotes.


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BIBLIOGRAPHY

BOOKS: Watson, (2008) Molecular Biology of the Gene (VI Edition). Cold spring harbour

lab.Press,Pearson Pub Becker, (2009). The world of the cell.(VII

Edition. Pearson Benjamin Cummings publishing, San Francisco.

ONLINE REFERENCE USED: Google search engine

structure of dna and rna by shirohi

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