DNA StructureComposition Taryono Faculty of Agriculture Gadjah Mada

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DNA Structure/Composition Taryono Faculty of Agriculture Gadjah Mada University

DNA Structure/Composition Taryono Faculty of Agriculture Gadjah Mada University

Flow of Genetic Information RNA Transcription DNA Replication Protein Translation

Flow of Genetic Information RNA Transcription DNA Replication Protein Translation

DNA Discovery of the DNA double helix A. 1950’s B. Rosalind Franklin - X-ray

DNA 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 The

DNA is the Genetic Material DNA encodes all the information in the cell 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 In some viruses the genetic material is RNA

How is Information Encoded in DNA? DNA Consists of four kinds of bases (A,

How is Information Encoded in DNA? 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 Two complementary strands of bases (C-G) and (A-T)

DNA is a Polymer of Deoxyribonucleotide Units DEOXYRIBONUCLEOTIDE DEOXY RIBO NUCLEOTIDE

DNA is a Polymer of Deoxyribonucleotide Units DEOXYRIBONUCLEOTIDE DEOXY RIBO NUCLEOTIDE

Deoxyribonucleic Acid (DNA) Nucleotide: 1. Phosphate group 2. 5 -carbon sugar 3. Nitrogenous base

Deoxyribonucleic Acid (DNA) Nucleotide: 1. Phosphate group 2. 5 -carbon sugar 3. Nitrogenous base ~2 nm wide

Phosphate Group O O=P-O O DNA Nucleotide 5 CH 2 O N C 1

Phosphate Group O O=P-O O DNA Nucleotide 5 CH 2 O N C 1 C 4 Sugar (deoxyribose) C 3 C 2 Nitrogenous base (A, G, C, or T)

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

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

DNA Double Helix 5 O 3 3 P 5 O O C G 1

DNA Double Helix 5 O 3 3 P 5 O O C G 1 P 5 3 2 4 4 2 3 P 1 T 5 A P 3 O O P 5 O 3 5 P

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

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

BASE-PAIRINGS Purines Pyrimidines Base Pairs Adenine (A) Thymine (T) A=T Guanine (G) Cytosine (C)

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

BASE-PAIRINGS H-bonds G C T A

BASE-PAIRINGS H-bonds G C T A

Chargaff’s Rule Adenine must pair with Thymine Guanine must pair with Cytosine Their amounts

Chargaff’s Rule Adenine must pair with Thymine Guanine must pair with Cytosine Their amounts in a given DNA molecule will be about the same. T A G C

Deoxy ribo nucleotide Ribose= Five Carbon Sugar Molecule 5´ 5´ 1´ 4´ 3´ 2´

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

5´ The DNA Backbone is a Deoxyribose Polymer 1´ 3´ 2´ Deoxyribose sugars are

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

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

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

Deoxy. Ribonucleotide Deoxyadenosine 5´-triphosphate (d. ATP) Deoxy. Ribonucleoside Deoxyadenosine

Deoxy. Ribonucleotide Deoxyadenosine 5´-triphosphate (d. ATP) Deoxy. Ribonucleoside Deoxyadenosine

DNA is Composed of Four Different Ribonucleotides 9 Adenine 1 Thymine Two Purines Two

DNA is Composed of Four Different Ribonucleotides 9 Adenine 1 Thymine Two Purines Two Pyrimidines 9 Guanine 1 Cytosine

T A C G T A 5´ 3´ 3´ 5´

T A C G T A 5´ 3´ 3´ 5´

Base Pairing Follows: Chargaff’s Rule: DNA has equal numbers of thiamines and adenines (A=T)

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) Note that in each pair there is one purine and one pyrimidine A-T G-C

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

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

G C = A T

G C = A T

Advantages of Double-Stranded Nature of DNA Forms a stable structure Hydrophobic bases stack on

Advantages of Double-Stranded Nature of DNA 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 For a new strand of DNA (replication) For an RNA molecule (transcription)

Double-stranded DNA Forms a Double Helix

Double-stranded DNA Forms a Double Helix

Native DNA Forms a B-DNA Helix Two strands wind about each other in a

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

DNA is Highly Packaged within the Cell If the DNA from a single human

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 DNA 2 M Cell Nucleus 5 x 10 -8 M (magnified lots of times)

Mechanisms of Packaging Has to be Organized so that DNA can be Untangled for

Mechanisms of Packaging 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

Supercoiling Most native DNA exists in a negatively supercoiled state This means that it

Supercoiling 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 They can make a cut in

Topoisomerases Modulate Supercoiling 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

DNA is Coiled Around Histone Proteins DNA is wrapped around abundant nuclear proteins called Histones This forms a complex called a Nucleosome Histones are H 1, H 2 A, H 2 B, H 3, H 4

DNA is Further Packaged

DNA is Further Packaged

Take Home Message DNA is a double helix composed of a sugarphosphate backbone and

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