Grade: Grade 9 Subject: Science Unit: Genetics SAT: ProblemSolving+DataAnalysis ACT: Science

DNA Replication

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DNA replication is the biological process by which a cell makes an identical copy of its DNA before cell division. This process ensures that genetic information is accurately passed from parent cells to daughter cells.

DNA Replication

DNA replication is the process of producing two identical copies of DNA from one original DNA molecule. It occurs during the S (synthesis) phase of the cell cycle and follows a semiconservative model.

Structure of DNA Review

To understand replication, recall the structure of DNA:

  • Double helix: Two strands wound around each other
  • Nucleotides: Building blocks containing a sugar, phosphate, and nitrogenous base
  • Base pairs: Adenine (A) pairs with Thymine (T); Guanine (G) pairs with Cytosine (C)
  • Antiparallel strands: One strand runs 5' to 3', the other runs 3' to 5'
  • Hydrogen bonds: Hold base pairs together (2 between A-T, 3 between G-C)

Semiconservative Replication

DNA replication is called semiconservative because each new DNA molecule contains:

  • One original (parent) strand
  • One newly synthesized (daughter) strand

This was proven by the Meselson-Stahl experiment in 1958.

Key Enzymes in DNA Replication

Enzyme Function
Helicase Unwinds and separates the double helix by breaking hydrogen bonds
Primase Synthesizes RNA primers to start replication
DNA Polymerase III Adds nucleotides to build new DNA strand (5' to 3' direction only)
DNA Polymerase I Removes RNA primers and replaces them with DNA
Ligase Joins Okazaki fragments and seals gaps in the sugar-phosphate backbone
Topoisomerase Relieves tension ahead of the replication fork by cutting and rejoining DNA
Single-strand binding proteins Keep separated strands apart and prevent re-annealing

Steps of DNA Replication

  1. Initiation: Helicase unwinds DNA at the origin of replication, creating a replication fork
  2. Primer synthesis: Primase adds short RNA primers to provide a starting point
  3. Elongation: DNA Polymerase III adds complementary nucleotides in the 5' to 3' direction
  4. Leading strand: Synthesized continuously toward the replication fork
  5. Lagging strand: Synthesized in short segments (Okazaki fragments) away from the fork
  6. Primer removal: DNA Polymerase I removes RNA primers and fills gaps with DNA
  7. Ligation: Ligase joins the fragments to create continuous strands

Leading vs. Lagging Strand

Because DNA polymerase can only add nucleotides in the 5' to 3' direction, the two strands are replicated differently. The leading strand is made continuously, while the lagging strand is made in short Okazaki fragments that must be joined together.

SAT/ACT Connection

Science passages may present diagrams of replication forks and ask you to identify enzyme functions, predict outcomes of enzyme mutations, or interpret data from replication experiments. Understanding the directional nature of synthesis (5' to 3') is key.

Examples

Example 1: Writing a Complementary Strand

Problem: Write the complementary strand for this DNA sequence: 5'-ATCGGCTA-3'

Step 1: Apply base pairing rules: A pairs with T, G pairs with C.

Step 2: Write the complementary bases: T-A-G-C-C-G-A-T

Step 3: Remember strands are antiparallel, so the complementary strand runs 3' to 5'.

Answer: 3'-TAGCCGAT-5' (or written as 5'-TAGCCGAT-3' reading in the opposite direction)

Example 2: Identifying Enzyme Function

Problem: A mutation prevents an enzyme from joining DNA fragments on the lagging strand. Which enzyme is affected?

Step 1: Identify what happens on the lagging strand - it's synthesized in Okazaki fragments.

Step 2: These fragments need to be joined together into a continuous strand.

Step 3: The enzyme that joins DNA fragments by forming phosphodiester bonds is ligase.

Answer: DNA ligase is the affected enzyme.

Example 3: Predicting Replication Products

Problem: A DNA molecule undergoes two rounds of replication. How many DNA molecules result, and how many contain only new strands?

Step 1: Start with 1 DNA molecule (2 strands: both original).

Step 2: After round 1: 2 DNA molecules (each has 1 original + 1 new strand).

Step 3: After round 2: 4 DNA molecules total.

Step 4: Of these 4: 2 have one original strand, 2 have only new strands.

Answer: 4 DNA molecules result; 2 contain only newly synthesized strands.

Example 4: Direction of Synthesis

Problem: The template strand reads 3'-GCATTAGC-5'. In which direction will the new strand be synthesized, and what will its sequence be?

Step 1: DNA polymerase always synthesizes in the 5' to 3' direction.

Step 2: The template is read 3' to 5', and the new strand is built 5' to 3'.

Step 3: Apply complementary base pairing to the template.

Step 4: G pairs with C, C pairs with G, A pairs with T, T pairs with A.

Answer: The new strand is synthesized 5' to 3' and reads: 5'-CGTAATCG-3'

Example 5: Calculating Generations

Problem: If you start with 1 DNA molecule and it replicates 5 times, how many DNA molecules will you have? How many will contain at least one original strand?

Step 1: Each replication doubles the number of molecules: 2^n where n = number of replications.

Step 2: After 5 replications: 2^5 = 32 DNA molecules.

Step 3: The original molecule had 2 strands. Due to semiconservative replication, these 2 original strands will each be in one molecule.

Step 4: No matter how many replications, only 2 molecules will contain an original strand.

Answer: 32 total DNA molecules; only 2 will contain an original strand.

Practice

Test your understanding of DNA replication with these questions.

1. What type of bond does helicase break to separate DNA strands?

A) Covalent bonds B) Hydrogen bonds C) Phosphodiester bonds D) Ionic bonds

2. Why are RNA primers necessary for DNA replication?

A) DNA polymerase cannot start synthesis from scratch B) They protect the DNA from damage C) They speed up the reaction D) They are not actually necessary

3. What is the name of the short DNA fragments synthesized on the lagging strand?

A) Watson fragments B) Crick segments C) Okazaki fragments D) Meselson pieces

4. In which direction does DNA polymerase synthesize new DNA?

A) 3' to 5' B) 5' to 3' C) Both directions D) It varies by strand

5. What is the complementary sequence to 5'-AATTGC-3'?

A) 5'-TTAACG-3' B) 3'-TTAACG-5' C) 5'-GCAATT-3' D) 3'-GCAATT-5'

6. Which enzyme removes RNA primers and replaces them with DNA?

A) Helicase B) Ligase C) DNA Polymerase I D) Primase

7. Why is replication called "semiconservative"?

A) Half the nucleotides are reused B) Each new molecule has one old and one new strand C) Only half the DNA is replicated D) The process uses half the normal energy

8. What would happen if ligase were not functioning?

A) DNA strands couldn't separate B) Primers couldn't be made C) Okazaki fragments couldn't be joined D) Nucleotides couldn't be added

9. Where does DNA replication begin?

A) Randomly along the chromosome B) At the origin of replication C) At the telomeres D) At the centromere

10. How many hydrogen bonds form between guanine and cytosine?

A) 1 B) 2 C) 3 D) 4

Click to reveal answers
  1. B) Hydrogen bonds - Helicase breaks the hydrogen bonds between complementary base pairs to separate the two strands.
  2. A) DNA polymerase cannot start synthesis from scratch - DNA polymerase can only add nucleotides to an existing 3' OH group, so primers provide a starting point.
  3. C) Okazaki fragments - Named after Reiji Okazaki who discovered them, these are short DNA segments on the lagging strand.
  4. B) 5' to 3' - DNA polymerase always adds new nucleotides to the 3' end, building in the 5' to 3' direction.
  5. C) 5'-GCAATT-3' - The complementary strand runs antiparallel, so 3'-TTAACG-5' is equivalent to 5'-GCAATT-3'.
  6. C) DNA Polymerase I - This enzyme has exonuclease activity that removes RNA primers and polymerase activity to fill in with DNA.
  7. B) Each new molecule has one old and one new strand - This is the definition of semiconservative replication.
  8. C) Okazaki fragments couldn't be joined - Ligase seals the nicks between fragments to create a continuous strand.
  9. B) At the origin of replication - Specific sequences called origins are where replication machinery assembles.
  10. C) 3 - G-C pairs have three hydrogen bonds, while A-T pairs have only two, making G-C bonds stronger.

Check Your Understanding

1. Explain why the lagging strand must be synthesized in fragments while the leading strand can be synthesized continuously.

Reveal Answer

DNA polymerase can only add nucleotides in the 5' to 3' direction. The leading strand's template runs 3' to 5' toward the replication fork, so polymerase can follow the fork continuously. However, the lagging strand's template runs 5' to 3' toward the fork, so polymerase must work in the opposite direction. As the fork opens, new sections of template are exposed behind the polymerase, requiring new primers and creating discontinuous Okazaki fragments.

2. What would be the consequence of a mutation that made DNA polymerase unable to proofread?

Reveal Answer

DNA polymerase has proofreading ability (3' to 5' exonuclease activity) that allows it to detect and correct mismatched base pairs. Without proofreading, the mutation rate would increase dramatically because incorrectly paired nucleotides would not be removed and replaced. This could lead to accumulation of harmful mutations, potentially causing cell death, cancer, or genetic diseases in offspring.

3. Why do cells need to replicate their DNA before cell division?

Reveal Answer

DNA contains the genetic instructions needed for cell function. When a cell divides, each daughter cell needs a complete copy of the genetic information. Replication ensures that both daughter cells receive identical genetic material. Without replication, daughter cells would have incomplete genetic information and could not function properly or would die.

4. How does the structure of DNA (specifically the antiparallel arrangement) create challenges for the replication machinery?

Reveal Answer

Because DNA strands run antiparallel (one 5' to 3', the other 3' to 5') and DNA polymerase only works 5' to 3', the two strands cannot be replicated in the same way. The leading strand template (3' to 5') allows continuous synthesis toward the fork. The lagging strand template (5' to 3') requires synthesis away from the fork in fragments. This necessitates multiple primers, Okazaki fragments, and the enzyme ligase to join fragments - making lagging strand synthesis more complex and slower.

🚀 Next Steps

  • Review any concepts that felt challenging
  • Move on to the next lesson when ready
  • Return to practice problems periodically for review