DNA Replication

State the components of a nucleotide

1. Phosphate group.

2. Pentose sugar.

3. Nitrogenous base.

Explain why DNA is less reactive than RNA

1. DNA is less reactive than RNA due to the absence of a hydroxyl group at carbon two in deoxyribose sugar.

2. In deoxyribose, carbon two is attached to a hydrogen atom while in ribose, carbon two is attached to a hydroxyl group.

State the difference between purines and pyrimidines

1. Purines such as adenine and guanine have two rings while pyrimidines such as thymine, cytosine and uracil have one ring.

Describe how polynucleotides are formed

1. Polynucleotides are formed by joining nucleotides together.

2. A phosphodiester bond is formed via a condensation reaction between the -OH group on carbon three of a pentose sugar of a nucleotide and the phosphate group on carbon 5 of a pentose sugar of an adjacent nucleotide, with the removal of one molecule of water.

3. Addition of many nucleotides produces a long polynucleotide chain with a backbone of alternating sugar and phosphate groups and bases projecting sideways from the sugars.

Describe the role of DNA

1. DNA functions as genetic material that is passed from one generation of cells to the next.

2. It also functions to store genetic information for gene expression.

Describe how the structure of DNA ensures accurate DNA replication and DNA repair

1. Each DNA molecule is a double helix consisting of two strands.

2. Each DNA parental strand acts as a template for synthesis of the daughter strand.

3. This ensures accurate replication so that the daughter cells have identical DNA molecules as the parent cell.

4. Each DNA parental strand also acts as a template for proofreading and repair of a damaged strand if mutation occurs, so that the DNA sequence can be maintained.

Describe how the structure of DNA ensures stability of hereditary material

1. Anti-parallel strands. This allows many hydrogen bonds to form between complementary bases and hold the two polynucleotide chains together.

2. Complementary base pairing between purines and pyrimidines. This holds the two polynucleotide chains together. This ensures a constant width of 2.0nm maintaining a stable structure. This stable structure maintains DNA sequence throughout the lifespan of the cell. This allows each DNA parental strand to act as a template for synthesis of the daughter strand. This ensures accurate DNA replication so that the daughter cells have identical DNA molecules as the parent cell.

3. Stacked nitrogenous bases. This allows hydrophobic interactions to form between stacked bases to maintain a stable structure.

4. Deoxyribose sugar in DNA. Deoxyribose is less reactive and more resistant to hydrolysis. This maintains DNA sequence throughout the lifespan of the cell.

5. Phosphodiester bonds. Phosphodiester bonds are strong covalent bonds to maintain a stable structure.

Describe how the structure of DNA enables it to store genetic information for gene expression

1. Sequence of bases forms genes. Genes code for functional gene products such as polypeptides, tRNA and rRNA.

2. Major and minor grooves formed from wind of DNA molecule. Major grooves allows for binding of proteins that regulate gene expression.

Explain why DNA replication is semi-conservative

1. After hydrogen bonds between complementary bases break and the two DNA parental strands separate, each DNA parental strand acts as a template to synthesise a new daughter strand.

2. Each new DNA molecule is a hybrid of one parental strand and one daughter strand, which will wind to form a double helix.

Describe what happens during the separation of the double helix

1. Helicase binds to DNA molecule at the origin of replication and disrupts hydrogen bonds between complementary bases, causing the two DNA parental strands to separate.

1. Single-stranded binding proteins stabilise the unwound helix by preventing rewinding of the DNA double helix.

2. A replication bubble with two Y-shaped replication forks are formed.

3. Replication proceeds in both directions until the entire DNA molecule is replicated.

Describe what happens during the synthesis of RNA primers

1. Primase synthesises RNA primers using free RNA nucleotides from 5’ to 3’.

2. This occurs via complementary base pairing with the DNA parental strand which acts as a template.

Explain why primers are needed for DNA synthesis

1. DNA polymerase cannot initiate DNA synthesise but can only add DNA nucleotides to an existing 3’-OH end of an existing strand from 5’ to 3’.

2. Shape of DNA polymerase active site is complementary to shape of 5’ phosphate group of an incoming nucleotide and 3’-OH group of the last nucleotide of the growing daughter strand.

3. Therefore, primers provide the free 3-OH end for DNA polymerase to add DNA nucleotides.

Describe what happens during the synthesis of DNA daughter strands

1. DNA polymerase reads the DNA template strand from 3’ to 5’ and synthesises the daughter strand from 5’ to 3’.

2. Free DNA nucleotides base pair with the DNA template strand via complementary base pairing.

3. Adenine base pairs with thymine and vice versa.

4. Guanine base pairs with cytosine and vice versa.

5. DNA polymerase catalyses the formation of phosphodiester bonds between adjacent DNA nucleotides.

6. DNA polymerase also proofreads as it synthesises the daughter strand.

7. If a nucleotide in the daughter strand is wrongly paired with the DNA template, DNA polymerase will remove and replace it with the correct nucleotide.

Describe what happens during the synthesis of the leading and lagging strands

1. Since the two DNA parental strands are anti-parallel, the two daughter strands (leading and lagging strands) are synthesised in opposite directions by DNA polymerase.

2. The leading strand is synthesised continuous towards the replication fork.

3. Only one primer is needed at the origin of replication.

4. DNA polymerase adds new DNA nucleotides from 5’ to 3’ without any breaks.

5. The lagging strands is synthesised discontinuously as Okazaki fragments away from the replication fork.

6. As helicase separates the two DNA parental strands to expose the DNA template, new primers will be synthesised by primase.

7. DNA polymerase adds new DNA nucleotides from 5’ to 3’, hence forming Okazaki fragments.

Describe what happens during the replacement of RNA primers with DNA

1. Another DNA polymerase replaces the RNA primers with DNA nucleotides.

2. DNA ligase seals the gaps by catalysing the formation of phosphodiester bonds between them.

3. At the end, two DNA molecules are formed.

4. Each DNA molecule consists of one parental strand and one daughter strand, which will wind together to form a double helix.

Describe what is the end replication problem

1. It is the shortening of DNA molecule after each round of DNA replication.

2. This is due to a gap at the 5’ end of the daughter strand after removal of RNA primer located at the 5’ end of the daughter strand.

3. The RNA primer cannot be replaced with DNA nucleotides because there is no existing 3’-OH end available for DNA polymerase to add DNA nucleotides.

4. DNA polymerase can only add DNA nucleotides to an existing 3’-OH end.

Describe the important features of DNA polymerase

1. DNA polymerase catalyses the formation of phosphodiester bonds between adjacent DNA nucleotides.

2. DNA polymerase cannot initiate DNA synthesise but can only add DNA nucleotides to 3’-OH end of an existing strand from 5’ to 3’.

3. Shape of DNA polymerase active site is complementary to shape of 5’ phosphate group of an incoming nucleotide and 3’-OH end of the last nucleotide of the growing daughter strand.

4. Therefore, primers provide the free 3’-OH end for DNA polymerase to add DNA nucleotides.

5. DNA polymerase reads the bases on DNA from 3’ to 5’ and synthesises the daughter strand from 5’ to 3’.

6. DNA polymerase has proofreading ability as it has 3’ to 5’ exonuclease activity.

Explain why one daughter strand is synthesised continuously while the other is synthesised discontinuously

1. The two DNA parental strands are anti-parallel.

2. Synthesis of DNA daughter strands always starts at the origin of replication.

3. DNA polymerase has an active site that can only add DNA nucleotides to 3’-OH end of an existing strand.

4. Therefore, DNA can only synthesise daughter strands from 5’ to 3’.

5. The leading strand is synthesised continuously towards the replication fork.

6. The lagging strand is synthesised discontinuously as Okazaki fragments away from the replication fork before they are joined together by DNA ligase.