Biology Chapter 1: DNA Replication & Repair
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Questions and Answers

What is the characteristic feature of the strands in a DNA double helix?

  • They run in opposite directions. (correct)
  • They are both 5’-P oriented.
  • They run in the same direction.
  • They are parallel to each other.

Which type of groove in B-form DNA is crucial for protein binding?

  • Minor groove
  • Severe groove
  • Major groove (correct)
  • Intermediate groove

What distance is observed between each base pair in DNA?

  • 5.0 Å
  • 4.6 Å
  • 2.0 Å
  • 3.4 Å (correct)

How are the bases bonded to the sugar in DNA structured?

<p>The bonds are consistently located, maintaining a stable backbone structure. (C)</p> Signup and view all the answers

What defines the architectural difference between the A-form and B-form DNA?

<p>The sugar pucker conformation. (C)</p> Signup and view all the answers

What is the width of the DNA double helix in B-form structure?

<p>20 Å (A)</p> Signup and view all the answers

In which conditions is the B-form of DNA most prevalent?

<p>Physiological cellular conditions. (B)</p> Signup and view all the answers

What type of interactions stabilize base stacking in the B-form of DNA?

<p>Van der Waals interactions (A)</p> Signup and view all the answers

What does the Meselson-Stahl experiment demonstrate about DNA replication?

<p>DNA replication is semi-conservative. (D)</p> Signup and view all the answers

What challenges arise due to the double helical structure of DNA during replication?

<p>DNA must be unwound to separate strands. (A)</p> Signup and view all the answers

What was the initial nitrogen isotope used in the Meselson-Stahl experiment?

<p>Nitrogen 15 (D)</p> Signup and view all the answers

What proportion of errors occurs in DNA replication?

<p>One in every ten billion nucleotides copied. (D)</p> Signup and view all the answers

What is required to melt the stable duplex structure of DNA?

<p>Energy to break hydrogen bonds. (C)</p> Signup and view all the answers

What additional consideration must be taken into account during DNA replication apart from copying the DNA?

<p>Repairing DNA damage. (C)</p> Signup and view all the answers

Which part of the glucocorticoid receptor interacts with DNA?

<p>The DNA-binding domain. (D)</p> Signup and view all the answers

How long does it take for a bacterial genome with 4.6 million base pairs to be copied?

<p>20 minutes (A)</p> Signup and view all the answers

What marks the parental strand during DNA replication in E.coli?

<p>Methylation of the parental strand (D)</p> Signup and view all the answers

Which protein is responsible for recognizing mismatches in DNA?

<p>MutS (D)</p> Signup and view all the answers

What role does the exonuclease play in the mismatch repair process?

<p>Removes the erroneous portion of the DNA strand (D)</p> Signup and view all the answers

What occurs during DNA recombination that contributes to genetic diversity?

<p>Exchange of genetic material between DNA molecules (A)</p> Signup and view all the answers

How does the helicase contribute to the mismatch repair mechanism?

<p>It unwinds the double-stranded DNA (A)</p> Signup and view all the answers

Which of these cancers is associated with defects in mismatch repair components?

<p>Colorectal cancer (C)</p> Signup and view all the answers

What is the role of DNA ligase in the mismatch repair process?

<p>To seal the remaining strand break (A)</p> Signup and view all the answers

What is a Holliday junction?

<p>A key intermediate in the DNA recombination process (C)</p> Signup and view all the answers

What is the main function of DNA polymerase III in DNA replication?

<p>To synthesize new DNA strands by adding nucleotides (A)</p> Signup and view all the answers

In the Trombone Model of DNA replication, the leading strand and the lagging strand are replicated how?

<p>Simultaneously, with the lagging strand forming loops (A)</p> Signup and view all the answers

What is the error rate of DNA polymerases during DNA replication?

<p>1 in 10000 (B)</p> Signup and view all the answers

How are Okazaki fragments formed during DNA replication?

<p>By discontinuous synthesis on the lagging strand (B)</p> Signup and view all the answers

During circular DNA replication, what happens at the origin of replication?

<p>Replication bubbles begin to form (C)</p> Signup and view all the answers

What is the role of the built-in exonuclease activity of DNA polymerase III?

<p>To remove incorrect nucleotides during replication (A)</p> Signup and view all the answers

What is a primary factor contributing to the high accuracy of DNA replication?

<p>The selection of complementary nucleotides (C)</p> Signup and view all the answers

What does the Trombone Model of DNA replication illustrate about the structure of the replisome?

<p>It operates as a single machine with two DNA polymerase III holoenzymes (D)</p> Signup and view all the answers

What role do topoisomerases play in the process of DNA replication?

<p>They introduce negative supercoils. (D)</p> Signup and view all the answers

Which enzyme is primarily responsible for synthesizing a primer during DNA replication?

<p>Primase (C)</p> Signup and view all the answers

How does negative supercoiling benefit thermophilic archaea?

<p>It stabilizes their DNA at high temperatures. (C)</p> Signup and view all the answers

In which direction does DNA polymerase III synthesize DNA?

<p>5' to 3' (D)</p> Signup and view all the answers

What is the primary function of the RNA primer in DNA replication?

<p>To initiate DNA synthesis with accurate nucleotides. (C)</p> Signup and view all the answers

Which of the following accurately describes the shape of DNA polymerases?

<p>They resemble a right hand. (B)</p> Signup and view all the answers

After the RNA primer is synthesized, what happens next in DNA replication?

<p>DNA polymerase uses the RNA primer to begin DNA synthesis. (C)</p> Signup and view all the answers

Which enzyme is responsible for relaxing supercoiled DNA during replication?

<p>Topoisomerase I (B)</p> Signup and view all the answers

What is required for the initiation of DNA synthesis?

<p>An RNA primer synthesized by a primase (A)</p> Signup and view all the answers

In which direction does the synthesis of DNA occur?

<p>From 5' to 3' (C)</p> Signup and view all the answers

What happens to the bond between the alpha and beta phosphates during the DNA synthesis reaction?

<p>It is broken. (A)</p> Signup and view all the answers

Which enzyme is responsible for unwinding DNA at the origins of replication?

<p>Helicase (A)</p> Signup and view all the answers

What component is necessary for the formation of the phosphate backbone during DNA synthesis?

<p>Nucleotide triphosphate substrates (D)</p> Signup and view all the answers

Why can DNA replication only proceed in one direction?

<p>Because the DNA template is read from 3' to 5' (A)</p> Signup and view all the answers

What type of bond is formed between the phosphate and sugar during nucleotide incorporation?

<p>Ester bond (A)</p> Signup and view all the answers

Which statement is true regarding the primer used in DNA synthesis?

<p>It is synthesized by a primase and later removed. (C)</p> Signup and view all the answers

Flashcards

DNA Strands

Two complementary DNA strands run in opposite directions, forming a double helix.

Base Pairing

The distance between each base pair in B-form DNA is 3.4 Å, allowing for base stacking and van der Waals interactions.

DNA Turn

A 36-degree turn occurs between each base pair, resulting in one full turn of DNA after 10 steps (~20 Å width).

B-form DNA

The most common form of DNA under physiological conditions, characterized by a large shallow major groove and a deep minor groove.

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A-form DNA

A form of DNA with a narrower and deeper major groove, less common than B-form DNA.

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DNA Backbone

The sugar-phosphate backbone remains relatively consistent regardless of the sequence due to the bonds always forming at the same position.

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Major Groove

The wider, shallow groove in B-form DNA, exposed to the cell's interior and allows for protein binding.

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Sequence-Specific Recognition

Proteins bind to the major groove of DNA, recognizing specific base sequences to regulate gene expression.

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DNA Polymerase Active Site

The region on DNA polymerase where nucleotide addition occurs, located at the base of the enzyme's 'palm' structure.

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Primer

A short RNA sequence that initiates DNA synthesis by providing a 3' hydroxyl group for the first nucleotide to attach to.

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5' to 3' Synthesis

The direction in which DNA and RNA are synthesized, adding new nucleotides to the 3' end of the growing strand.

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Nucleotide Triphosphate Hydrolysis

The process of breaking a phosphate bond in a nucleotide triphosphate, releasing energy and providing a phosphate group for DNA/RNA synthesis.

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DNA Template Strand

The existing strand of DNA that serves as a guide for the synthesis of a new complementary strand.

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Origin of Replication

Specific DNA sequences where DNA replication begins, marking the start of 'replication bubbles'.

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Helicase

An enzyme that unwinds the DNA double helix, creating a replication bubble with two 'forks'.

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Replication Fork

A Y-shaped point where DNA unwinding and new strand synthesis occur during DNA replication.

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DNA Structure

DNA's double helix shape has specific geometries. The major groove exposes nucleotides for recognition by proteins like transcription factors.

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Semi-Conservative Replication

During DNA replication, each new DNA molecule is made up of one original strand and one newly synthesized strand.

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Meselson-Stahl Experiment

This experiment used isotopes of nitrogen to prove that DNA replication is semi-conservative. Bacteria grown in heavy nitrogen (N15) were switched to light nitrogen (N14) and the density of DNA was measured.

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DNA Topological Problem

Unwinding DNA for replication creates tension and overwinding downstream.

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DNA Stability

DNA is a stable molecule due to strong hydrogen bonds and stacking interactions between bases.

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Energy Needs

Melting DNA for replication requires energy because of the strong hydrogen bonds.

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Replication Accuracy

DNA replication is incredibly accurate, with very few errors.

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DNA Repair

Damaged DNA must be repaired to maintain the integrity of the genome.

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Topoisomerase

An enzyme that can both relax and supercoil DNA by introducing cuts and twisting the molecule, using ATP for the latter process.

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Negative Supercoiling

A type of DNA coiling where the double helix twists in the opposite direction from its normal helical turn, resulting in the helix being more compact.

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DNA Replication

The process of copying DNA, using a template strand to produce a complementary DNA strand.

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RNA Primer

A short RNA molecule that initiates DNA replication by providing a starting point for DNA polymerase.

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DNA Polymerase III

The primary DNA polymerase in bacterial cells, responsible for copying DNA from 5' to 3', using an RNA primer.

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DNA Polymerase Architecture

The structural organization of DNA polymerases resembling a right hand with 'fingers' and 'thumb' forming a cleft that binds DNA.

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Why Is a Primer Needed?

Primers increase the accuracy of DNA replication by providing a starting point and ensuring the incorporation of the first few nucleotides is more precise.

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Leading Strand

The strand of DNA that is synthesized continuously during replication, moving in the same direction as the replication fork.

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Lagging Strand

The strand of DNA synthesized discontinuously during replication, moving in the opposite direction of the replication fork.

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Okazaki Fragments

Short, newly synthesized DNA fragments created on the lagging strand during replication.

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Trombone Model

A model of DNA replication where the leading and lagging strands are synthesized simultaneously by a single 'replisome' containing two DNA polymerase III holoenzymes.

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Replisome

A complex of proteins involved in DNA replication, including two DNA polymerase III holoenzymes.

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Exonuclease Activity

The ability of some DNA polymerases to remove nucleotides from the end of a DNA strand, which is essential for proofreading and repairing errors.

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Mismatch Repair (MMR)

A cellular process that corrects errors in DNA replication, such as mismatched base pairs, by recognizing and removing the incorrect nucleotide from the newly synthesized strand.

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MutH

An endonuclease in the MMR system that specifically recognizes hemimethylated DNA, cutting the unmethylated daughter strand near the mismatch.

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Hemimethylated DNA

DNA where one strand is methylated, while the other is not. This is a marker of newly replicated DNA.

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How MMR repairs errors

  1. MutS recognizes the mismatch. 2. MutL recruits MutH. 3. MutH cuts the unmethylated strand. 4. Helicase unwinds. 5. Exonuclease removes the error. 6. DNA polymerase fills the gap. 7. Ligase seals the break.
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DNA recombination

The exchange of genetic material between two DNA molecules, creating new combinations of alleles and contributing to genetic diversity.

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Holliday junction

A key intermediate structure in DNA recombination, formed by the pairing of four strands of DNA, resembling a cross.

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Homologous recombination

A type of DNA recombination that occurs between similar DNA sequences, essential for DNA repair.

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Site-specific recombination

A type of DNA recombination where specific DNA sequences are inserted at target sites in the genome, often used by viruses.

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Study Notes

Fundamentals in Biology 1: From Molecules to the Biochemistry of Cells

  • This document is for internal use only at ETH Zurich.

Part 1: Introduction to DNA Replication, Recombination and Repair

  • DNA replication is a highly accurate biological process.
  • Error rate is 1 in 10 billion cases.
  • Accuracy achieved through accurate synthesis and proofreading methods, and subsequent repairs.

DNA Replication

  • The Central Dogma of Molecular Biology describes the expression of genetic information from DNA to RNA to protein.
  • DNA replication is crucial to understanding the expression of genetic information.
  • DNA replication and preservation of genetic information between generations occur accurately at a high rate.

Friedrich Miescher's Discovery of DNA

  • In the 1860s, Friedrich Miescher discovered DNA in bandages from injured people.
  • He isolated a substance (nuclein) in the nucleus different from proteins.
  • Nuclein contained phosphorus and nitrogen, but not sulfur.
  • At low pH, the macromolecule (DNA) became insoluble, suggesting it is an acid.

Alfred Hershey and Martha Chase's Experiment

  • In 1952, they demonstrated that DNA carries genetic information.
  • The experiment used bacteriophages (bacterial viruses) with either protein or DNA labelled with radioactive isotopes.
  • Only radioactively labelled DNA entered bacterial cells.
  • This confirmed DNA was the genetic material.

Chargaff's Nucleotide Ratios ("Chargaff's Rules")

  • Erwin Chargaff used chromatography and spectrophotometry to analyze nucleotide composition in DNA from different organisms.
  • The amount of individual nucleotides varied between species, but the ratio of adenine to thymine and guanine to cytosine was always equimolar.

Watson and Crick's Model of DNA's Structure

  • Watson and Crick used models to deduce DNA's structure.
  • Base pairs (G:C and A:T) form, maintaining consistent width.
  • DNA's sequence can be deduced from one strand.

DNA Structure

  • DNA structure forms a double helix.
  • Two strands are antiparallel (5' to 3' and 3' to 5').
  • Sugar-phosphate backbone is on the outside.
  • Bases (A, T, G, C) are on the inside.
  • Base pairing (A with T, G with C).
  • Specific helical pitches.
  • 3.4 Å distance between base pairs.
  • 36° turn between each base pair.

DNA's Topological Problem

  • DNA's helical structure presents topological problems for copying.
  • Unwinding creates overwinding.
  • Energy is required to melt the DNA.
  • Replication happens very quickly.
  • Topoisomerase enzymes solve these problems by cutting, rotating, and rejoining DNA strands.

DNA Polymerases and the Need for a Primase

  • DNA polymerases copy DNA with high accuracy (1 error per 10 billion nucleotides).
  • DNA polymerase III is the main polymerase in bacteria.
  • DNA polymerase requires a primer to start replication, which is synthesized by primase.
  • Primers are short RNA sequences.
  • RNA primers are later replaced with DNA.

Replication Fork Formation and Okazaki Fragments

  • DNA replication occurs at replication forks.
  • Leading strand is replicated continuously.
  • Lagging strand is replicated discontinuously as Okazaki fragments.
  • Okazaki fragments are later joined by DNA ligase.

The Trombone Model of DNA Replication

  • The leading and lagging strands are replicated simultaneously.
  • One strand loops, similar to a trombone slide.

Circular DNA Replication

  • Replication starts at the origin of replication and proceeds in opposite directions.

DNA Repair and Recombination

Introduction

  • DNA polymerases have high accuracy during DNA replication.
  • However, errors do happen.
  • Repair mechanisms correct these errors.
  • Recombination is a key process in generating genetic diversity and DNA repair.

DNA Repair Mechanisms

  • Nucleotide excision repair (NER) corrects bulky DNA lesions.
  • Base excision repair (BER) corrects damaged/mismatched bases.
  • Mismatch repair (MMR) corrects mismatched bases, insertions, and deletions.

Spontaneous DNA Mutations

  • Spontaneous mutations (e.g., transversions, transitions, insertions, and deletions) can occur.
  • These mutations can be corrected.

DNA Recombination

  • DNA recombination is crucial for genetic diversity and DNA repair.
  • It involves the exchange of DNA segments between DNA molecules.
  • A Holliday junction is a key intermediate structure.
  • Homologous recombination repairs double-strand breaks.
  • Site-specific recombination is used by certain enzymes like Cre recombinase.

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Fundamentals in Biology 1: From Molecules to the Biochemistry of Cells PDF

Description

Explore the fundamentals of DNA replication, recombination, and repair in this quiz. Understand the accuracy of these processes and the historical discovery of DNA by Friedrich Miescher. Test your knowledge on the principles guiding the expression of genetic information.

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