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G11_Bio session 3
Content
1) DNA structure, analysis and nucleotide
2) 3D shape deducing
3) DNA vs RNA
4) DNA replication main steps
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❖ DNA structure, analysis and nucleotide
Base Composition Analysis
➢ Chargaff analyzed DNA base composition in various organisms.
➢ In 1950, he reported that DNA base composition differs between species.
• Example: Human DNA contains 30.3% adenine (A), while E. coli contains 26.0%
adenine (A).
➢ This discovery highlighted molecular diversity in DNA, suggesting it as a credible candidate
for genetic material.
Nucleotide Ratios
➢ Chargaff observed a regularity in nucleotide base ratios across species:
• Adenine (A) = Thymine (T)
• Guanine (G) = Cytosine (C)
Chargaff’s Rules
➢ Two key findings emerged, known as Chargaff’s rules:
1) The base composition varies among species.
2) Within a species, A = T and G = C.
➢ These rules were not explained until the discovery of the double helix structure of DNA.
Example of Human DNA Base Percentages
➢ Adenine (A): 30.3%
➢ Thymine (T): 30.3%
➢ Guanine (G): 19.5%
➢ Cytosine (C): 19.9%
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❖ 3D shape of DNA
Challenge of DNA Structure and Inheritance
➢ After confirming that DNA is the genetic material, scientists sought to understand how its
structure relates to inheritance.
➢ By the early 1950s, the covalent bonds in nucleic acid polymers were known, but the three-
dimensional structure of DNA was still unclear.
Scientists Involved
➢ Notable scientists working on DNA structure:
• Linus Pauling (California Institute of Technology).
• Maurice Wilkins and Rosalind Franklin (King's College, London).
• James Watson and Francis Crick, relatively unknown at the time, were the first to solve
the structure.
Discovery of DNA's Double Helix Structure
➢ Watson saw an X-ray diffraction image of DNA from Rosalind Franklin while visiting
Maurice Wilkins.
• The diffraction pattern suggested that DNA is helical.
• Franklin’s data also indicated that the helix had two strands rather than three, leading to
the idea of the double helix.
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Watson and Crick's Model
➢ Watson and Crick built a double helix model based on:
• X-ray data from Franklin and others.
• Chargaff’s rules of base pairing.
➢ Franklin's work revealed the:
• sugar-phosphate backbones were on the outside
• nitrogenous bases on the inside.
• This arrangement protected hydrophobic bases from the surrounding aqueous
environment and avoided phosphate repulsion.
Antiparallel Structure
➢ The two sugar-phosphate backbones in the model were antiparallel, meaning their
subunits ran in opposite directions.
➢ The nitrogenous bases formed the rungs of the "ladder" (double helix), with the sugar-
phosphate backbones as the side ropes.
Dimensions of the Double Helix
➢ Franklin’s X-ray data showed:
• The helix makes one full turn every 3.4 nm.
• Base pairs are stacked 0.34 nm apart, creating 10 base pairs per turn.
Base Pairing in the Double Helix
➢ The nitrogenous bases pair specifically:
• Adenine (A) with Thymine (T).
• Guanine (G) with Cytosine (C).
➢ Watson and Crick initially thought bases paired like with like (A with A, C with C), but this
did not fit the data.
• Purines (A, G) are double-ringed, while Pyrimidines (C, T) are single-ringed.
• Purine-purine pairs are too wide, and pyrimidine-pyrimidine pairs are too narrow for
the 2-nm diameter of the helix.
• Pairing a purine with a pyrimidine gives the helix its uniform diameter.
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Base Pairing and Nucleotide Sequence Flexibility
➢ Base pairing rules determine the combinations of nitrogenous bases (A-T, G-C) in the
double helix.
➢ These rules do not restrict the sequence of nucleotides
along each DNA strand.
➢ The linear sequence of the four bases can vary widely,
giving each gene a unique base sequence.
DNA Facts
➢ Single human DNA strand: ~1 meter long.
➢ Total DNA per cell: ~2 meters.
➢ Nucleus diameter: 0.00034 mm.
➢ DNA contains ~3 billion base pairs.
➢ A person’s DNA sequence would fill 200 books of 1000 pages each.
Function of DNA
➢ Stores and transmits genetic information.
➢ Instructs cells on their functions.
DNA Structure
➢ Full name: Deoxyribonucleic Acid.
➢ Nucleotides consist of:
• 5-carbon sugar (deoxyribose).
• Phosphate group.
• Nitrogen base.
DNA Strand Formation
➢ Nucleotides form a polymer with sugar-phosphate covalent bonds.
➢ Nitrogen bases are connected by hydrogen bonds.
Anti-parallel Structure
➢ DNA strands run in opposite directions (5' and 3' ends).
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❖ DNA vs RNA
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Phosphodiester Bonds
➢ Phosphodiester bonds link the 5' carbon of one nucleotide to the 3' carbon of another.
➢ A covalent bond forms between the oxygen on the 3' carbon and the phosphate group on
the 5' carbon.
➢ DNA sequence example: 5' ATGC 3' pairs with 3' TACG 5'.
➢ The sugar-phosphate backbone grows in the 5' to 3' direction.
Macromolecules with Nucleotide Subunits
➢ Macromolecules are large molecules made of repeated subunits (monomers).
➢ Nucleic acids (DNA & RNA) are polymers of nucleotides linked by phosphodiester bonds.
➢ Proteins are polymers of amino acids joined by peptide bonds.
❖ DNA replication
DNA Replication Overview
➢ DNA is replicated before cell division to ensure each new cell gets a complete genetic copy.
➢ Watson and Crick noted that the complementary base-paired structure of DNA allows for
accurate replication.
➢ The nucleotide sequence of each strand guides the creation of its complementary partner.
Origins of Replication
➢ DNA replication begins at specific sites called origins of replication.
➢ Bacterial chromosomes (e.g., E. coli) have a single origin, while eukaryotic chromosomes
have multiple origins.
➢ Replication bubbles form and expand in both directions, speeding up the process.
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Unwinding the DNA
➢ Helicases unwind the double helix, separating the parental strands.
➢ Single-strand binding proteins prevent strands from re-pairing.
➢ Topoisomerase relieves strain ahead of the replication fork by breaking and rejoining DNA
strands.
Primers and Strand Synthesis
➢ Primase creates a short RNA primer to start DNA synthesis.
➢ DNA polymerase adds nucleotides to the RNA primer, forming the new DNA strand.
➢ DNA polymerase III in E. coli adds nucleotides at a rate of 500 per second, while in
humans, it's 50 per second.
Nucleoside Triphosphates and Energy
➢ Nucleoside triphosphates provide the building blocks for DNA, similar to ATP but with
deoxyribose instead of ribose.
➢ As each nucleotide is added, two phosphate groups are lost, releasing energy to drive the
polymerization reaction.
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Enzymes in DNA Replication
➢ Replication Process involves multiple enzymes and proteins working together.
1) DNA helicase unwinds the double helix by breaking hydrogen bonds between paired
bases.
2) DNA polymerase catalyzes the addition of nucleotides to the 3’ end of the new strand by
pairing them with the template strand.
Antiparallel Elongation
➢ DNA strands are antiparallel, meaning they run in opposite directions.
➢ DNA polymerase can only add nucleotides to the 3' end, so the new DNA strand elongates in
the 5' to 3' direction.
➢ The leading strand is synthesized continuously, while the lagging strand is synthesized
discontinuously in segments called Okazaki fragments.
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DNA Replication Complex
➢ Proteins involved in replication form a large complex called the DNA replication machine,
enhancing efficiency through protein-protein interactions.
➢ Recent studies suggest that DNA moves through the complex, not the other way around, with
DNA polymerase reeling in parental DNA and extruding daughter strands.
Proofreading and Repair
➢ DNA polymerases proofread nucleotides during replication, correcting mismatches.
➢ Initial pairing errors occur frequently, but proofreading reduces errors to about 1 in 10
billion nucleotides.
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