Lesson 1-3

1. Lesson 1-3 9 things you need to know about DNA Structure & Replication

2. James Watson and Francis Crick solved the structure of DNA using a wire frame model Watson and Crick the morning after publishing their conclusion in a 1 page article in Nature (April 23, 1953)

3. DNA is made from connecting Nucleotides into a strand This is a single nucleotide Each nucleotide contains a phosphate a sugar a nitrogenous base This short strands shows the four different nucleotides needed to make DNA 1. A nucleotide is composed of 3 parts

4. The phosphate and sugar groups are the same for all nucleotides The bases are different between nucleotides Thymine and Cytosine are pyrimidines meaning they have one ring Adenine and Guanine are Purines meaning they have two rings 2. Nucleotides differ in the Nitrogen bases. 1 1 1 1 2 2

5. The phosphate group from one nucleotide is linked to the bottom of the sugar by a covalent (strong) bond. 3. A single strand of DNA is made by linking nucleotides.

6. The repeating pattern of sugar-Phosphate is called the “backbone” The Bases stick out from the backbone 3. A single stand of DNA is made by linking nucleotides.

7. Note that the ends of the strand on the right are different. The top with the yellow phosphate group is called the 5’ (five prime) end. The bottom with the blue sugar is called the 3’ (three prime) end 5’ 4. A strand of DNA has a head and a tail. 3’

8. 4. A strand of DNA has a head and a tail. • The 3’ carbon is at the bottom of the molecule • The ‘ symbol is used to tell carbons in the sugar apart from those that are in the nitrogenous base. • The 5’ and 3’ names are based on the numbering around the sugar molecule. • The phosphate is attached to the 5’ carbon at the top of the molecule.

9. 5. A double helix is made by twisting two strands together

10. 5. A double helix is made by twisting two strands together • Sugar-phosphate back-bone forms sides of a ladder • Bases form a pair across the middle. • Bases held by weak hydrogen bonds

11. 5. A double helix is made by twisting two strands together • Sugar-phosphate back-bone forms sides of a ladder • Bases form a pair across the middle. • Bases held by weak hydrogen bonds

12. 6. The double helix makes one complete turn (twist) every 10 nucleotides • There are 0.34 nm between each base pair or 3.4nm for one full twist • How many nucleotides would fit in a strand that was 1 mm long? 1 m? (1mm = 1,000,000nm) • 1,000,000/0.34 = 2.9 million & 2.9 billion

13. 7. The double helix is the same width along its entire length (2 nm) 2 nm • Each base pair is made from 1 double ring and 1 single ring of bases • 2 single ring pairs or 2 double ring pairs would result in either a bump or a dip in the width. • Bumps and dips are often used by repair enzymes to identify mutations.

14. 8. Cytosine bases always pair with Guanine, Thymine always pairs with Adenine • Base pairs always have one purine (double ring, A or G) and one pyrimidine (single ring, C or T) • Three hydrogen fingers always pair with three hydrogen fingers (G & C), two with two. (A & T)

15. 9. The hydrogen bonds holding two strands together can be pulled apart • Hydrogen bonds are weak bonds and can be pulled apart separating the two strands. • The covalent bonds along each side do not break easily • DNA must be separated for important processes like replication and transcription

16. 10. DNA size is often described in terms of base pairs meaning an AT or GC pair. • One Base Pair is… • Base Pair is often abbreviated as bp • 1 Kb = 1000 bp • How many base pairs is the human genome? 3.2 billion bp

17. 9 things you need to know about REPLICATION

18. Replication Overview • Template strands separate • New nucleotides are added according to templates • New nucleotides are sealed into new strand

19. 1. Replication occurs just before cell division • Replication is the process of copying the genome. • It occurs during the S phase of the cell cycle • The cell divides the DNA and other cellular contents during Mitotic Phase

20. 2. To replicate the two strands of the double helix must first be split • Splitting the helix allows each old strand to serve as a template for building a new strand. • Splitting the helix can be done by increasing the temperature to 100°C (boiling)

21. 2. To replicate the two strands of the double helix must first be split • In the Cell splitting is performed by a protein called Helicase • Helicase – unwinds the DNA helix at 37°C (body temperature)

22. 3. Replication starts at sites along the chromosome called Origins of Replication • The origin is a specific sequence in the DNA that is recognized by DNA polymerase as a start point for replication • The origin is usually an AT rich region because AT base pairs are easier to pull apart than GC pairs. • There are many origins of replication in a single chromosome • Each replication event starts simultaneously

23. 4. Each strand provides a template for building a new strand • New nucleotides are arranged in the new strand by their ability to complement the template strand bases • G’s bind with C’s • A’s bind with T’s

24. 5. DNA Polymerase is needed to add and weld nucleotides into a new strand. • DNA polymerase adds about 1000-5000 bp/minute depending on conditions

25. 6. Replication can only occur in one direction. • New nucleotides add to 3’ OH group • Loss of two P from new nucleotide provides energy for new covalent bond formation

26. 6. Replication can only occur in one direction. Note that Polymerase is only adding to the 3’ end of the new (light blue) strand

27. 7. DNA polymerase cannot start a new strand. • We are not sure why but DNA polymerase does not have the ability to start a new strand of DNA by itself it can only add to an existing strand • In the Cell a short primer sequence is added by a enzyme called Primase. • A primer is a short sequence of nucleotides used by DNA polymerase as a starting point. • In the cell the Primer is actually made of RNA nucleotides and must be eventually removed and replaced with DNA

28. 7. DNA polymerase cannot start a new strand. • Students often confuse the terms primer and primase. Be sure you understand the difference Primase (pink): enzyme that adds Primers to the new strand Primers (red): short sequence of RNA nucleotides used as starting point for DNA polymerase

29. 8. Once a new strand is created it is proof-read for mistakes • Before editing the error rate is about 1/100,000 • After editing the error rate in replication is about 1/10,000,000 • These errors create mutations in the DNA from one generation to the next. • Mutations in the DNA are the source of variation in living organisms.

30. 9. Identify the components and what they do in replication

31. Test Your Comprehension Fill in the table with as many players in Replication you can recall from your reading. If possible write them in the order they participate in the process.

32. Replication Worksheet Fill in the table with as many players in Replication you can recall from your reading. If possible write them in the order they participate in the process.

33. Test your Critical Thinking What do you think would happen if … ? • No dCTP was present • Single stranded binding proteins were absent. • There were only a 1 or 2 Origins in the genome?