DNA Structure/Composition Taryono Faculty of Agriculture Gadjah Mada University

Flow of Genetic Information DNA Replication RNA Transcription Protein Translation

DNADNA Discovery of the DNA double helix Discovery of the DNA double helix A.1950’s B.Rosalind Franklin - X-ray photo of DNA. C.Watson and Crick - described the DNA molecule from Franklin’s X-ray.

DNA is the Genetic Material DNA encodes all the information in the cell DNA encodes all the information in the cell The composition of the DNA is the same in all cells within an organism The composition of the DNA is the same in all cells within an organism  Variation among different cells is achieved by reading the DNA differently DNA contains four bases that encode all the information to make a bacteria or a human DNA contains four bases that encode all the information to make a bacteria or a human In some viruses the genetic material is RNA In some viruses the genetic material is RNA

How is Information Encoded in DNA? DNA Consists of four kinds of bases (A,C,G,T) joined to a sugar phosphate backbone DNA Consists of four kinds of bases (A,C,G,T) joined to a sugar phosphate backbone Bases carry the genetic information while the phosphate backbone is structural Bases carry the genetic information while the phosphate backbone is structural Two complementary strands of bases (C-G) and (A-T) Two complementary strands of bases (C-G) and (A-T)

DNA is a Polymer of Deoxyribonucleotide Units DEOXYRIBONUCLEOTIDE

Deoxyribonucleic Acid (DNA) Nucleotide: 1.Phosphate group 2.5-carbon sugar 3.Nitrogenous base ~2 nm wide ~2 nm wide

DNA Nucleotide O O=P-O OPhosphate Group Group N Nitrogenous base (A, G, C, or T) (A, G, C, or T) CH2 O C1C1 C4C4 C3C3 C2C2 5 Sugar Sugar(deoxyribose)

DNA Double Helix Nitrogenous Base (A,T,G or C) “Rungs of ladder” “Legs of ladder” Phosphate & Sugar Backbone

DNA Double Helix P P P O O O P P P O O O G C TA

Nitrogenous Bases PURINES PURINES 1.Adenine (A) 2.Guanine (G) PYRIMIDINES PYRIMIDINES 3.Thymine (T) 4.Cytosine (C) T or C A or G

BASE-PAIRINGSBASE-PAIRINGS Base # of Purines PyrimidinesPairs H-Bonds Adenine (A) Thymine (T)A = T 2 Guanine (G) Cytosine (C)C G 3 CG 3 H-bonds

BASE-PAIRINGSBASE-PAIRINGS CG H-bonds T A

Chargaff’s Rule Adenine must pair with Thymine Adenine must pair with Thymine Guanine must pair with Cytosine Guanine must pair with Cytosine Their amounts in a given DNA molecule will be about the same. Their amounts in a given DNA molecule will be about the same. G C TA

Backbone Sugar Molecules Deoxyribose (DNA)Ribose (RNA) 1´ 2´ 3´ 4´ 5´ 1´ 2´ 3´ 4´ 5´ Ribose= Five Carbon Sugar Molecule Deoxy ribo nucleotide

The DNA Backbone is a Deoxyribose Polymer Deoxyribose sugars are linked by Phosphodiester Bonds 5´ 3´ 5´ 3´ 2´ 1´ 5´-p3´-OH 5´3´

5´ 3´ 5´ 3´5´ 3´ 5´ 3´ 5´ 3´ 2´ 1´

5´ 3´ 5´ 3´ 2´ 1´ Base 5´ 3´ 5´ 3´ 2´ 1´

(dATP) Deoxyadenosine 5´-triphosphate DeoxyRibonucleotide DeoxyRibonucleoside Deoxyadenosine

DNA is Composed of Four Different Ribonucleotides AdenineGuanine ThymineCytosine Two Purines Two Pyrimidines

5´ 3´5´ 3´ T C T A G A

Base Pairing Follows: Chargaff’s Rule: DNA has equal numbers of thiamines and adenines (A=T) and equal numbers of guanines and cytosines (G=C) DNA has equal numbers of thiamines and adenines (A=T) and equal numbers of guanines and cytosines (G=C) Note that in each pair there is one purine and one pyrimidine A-TG-C

Base Pairing Occurs Through Hydrogen Bonds A-T G-C

= GC AT

Advantages of Double-Stranded Nature of DNA Forms a stable structure Forms a stable structure  Hydrophobic bases stack on top of one another away from solvent  Charged phosphate backbone is on the outside accessible to solvent Each strand can serve as the template Each strand can serve as the template  For a new strand of DNA (replication)  For an RNA molecule (transcription)

Double-stranded DNA Forms a Double Helix

Native DNA Forms a B-DNA Helix Two strands wind about each other in a right-handed manner Two strands wind about each other in a right-handed manner Diameter: ~20Å Diameter: ~20Å Bases per turn: 10 (~34Å) Bases per turn: 10 (~34Å) A major and a minor groove A major and a minor groove 20Å Major Minor

DNA is Highly Packaged within the Cell If the DNA from a single human cell were stretched out end to end, it would be ~2 meters in length If the DNA from a single human cell were stretched out end to end, it would be ~2 meters in length Cell Nucleus 5 x M DNA 2 M (magnified lots of times)

Mechanisms of Packaging Has to be Organized so that DNA can be Untangled for Replication and Transcription Has to be Organized so that DNA can be Untangled for Replication and Transcription  Supercoiling  Wrapping around Proteins to Create Chromatin Enzymes that Modulate the Packaging of DNA are called Topoisomerases Enzymes that Modulate the Packaging of DNA are called Topoisomerases

Supercoiling Most native DNA exists in a negatively supercoiled state Most native DNA exists in a negatively supercoiled state  This means that it is slightly unwound and it is a bit easier to pull the two strands apart More supercoiling

Topoisomerases Modulate Supercoiling Topoisomerases act as Molecular Scissors Topoisomerases act as Molecular Scissors  They can make a cut in the DNA and pass second strand through that break to untangle the DNA

DNA is Coiled Around Histone Proteins DNA is wrapped around abundant nuclear proteins called Histones DNA is wrapped around abundant nuclear proteins called Histones This forms a complex called a Nucleosome This forms a complex called a Nucleosome Histones are H1, H2A, H2B, H3, H4 Histones are H1, H2A, H2B, H3, H4

DNA is Further Packaged

Take Home Message DNA is a double helix composed of a sugar- phosphate backbone and base pairs (a polymer of deoxyribonucleotides) DNA is a double helix composed of a sugar- phosphate backbone and base pairs (a polymer of deoxyribonucleotides) Composition/Structure Composition/Structure DNA is compacted to fit into the cell through: DNA is compacted to fit into the cell through:  Supercoiling  Extensive interactions with proteins These factors all contribute to how the DNA is Read These factors all contribute to how the DNA is Read