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?

The bonds are consistently located, maintaining a stable backbone structure. Signup and view all the answers

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

The sugar pucker conformation. Signup and view all the answers

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

20 Å Signup and view all the answers

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

Physiological cellular conditions. Signup and view all the answers

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

Van der Waals interactions Signup and view all the answers

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

DNA replication is semi-conservative. Signup and view all the answers

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

DNA must be unwound to separate strands. Signup and view all the answers

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

Nitrogen 15 Signup and view all the answers

What proportion of errors occurs in DNA replication?

One in every ten billion nucleotides copied. Signup and view all the answers

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

Energy to break hydrogen bonds. Signup and view all the answers

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

Repairing DNA damage. Signup and view all the answers

Which part of the glucocorticoid receptor interacts with DNA?

The DNA-binding domain. Signup and view all the answers

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

20 minutes Signup and view all the answers

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

Methylation of the parental strand Signup and view all the answers

Which protein is responsible for recognizing mismatches in DNA?

MutS Signup and view all the answers

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

Removes the erroneous portion of the DNA strand Signup and view all the answers

What occurs during DNA recombination that contributes to genetic diversity?

Exchange of genetic material between DNA molecules Signup and view all the answers

How does the helicase contribute to the mismatch repair mechanism?

It unwinds the double-stranded DNA Signup and view all the answers

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

Colorectal cancer Signup and view all the answers

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

To seal the remaining strand break Signup and view all the answers

What is a Holliday junction?

A key intermediate in the DNA recombination process Signup and view all the answers

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

To synthesize new DNA strands by adding nucleotides Signup and view all the answers

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

Simultaneously, with the lagging strand forming loops Signup and view all the answers

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

1 in 10000 Signup and view all the answers

How are Okazaki fragments formed during DNA replication?

By discontinuous synthesis on the lagging strand Signup and view all the answers

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

Replication bubbles begin to form Signup and view all the answers

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

To remove incorrect nucleotides during replication Signup and view all the answers

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

The selection of complementary nucleotides Signup and view all the answers

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

It operates as a single machine with two DNA polymerase III holoenzymes Signup and view all the answers

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

They introduce negative supercoils. Signup and view all the answers

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

Primase Signup and view all the answers

How does negative supercoiling benefit thermophilic archaea?

It stabilizes their DNA at high temperatures. Signup and view all the answers

In which direction does DNA polymerase III synthesize DNA?

5' to 3' Signup and view all the answers

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

To initiate DNA synthesis with accurate nucleotides. Signup and view all the answers

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

They resemble a right hand. Signup and view all the answers

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

DNA polymerase uses the RNA primer to begin DNA synthesis. Signup and view all the answers

Which enzyme is responsible for relaxing supercoiled DNA during replication?

Topoisomerase I Signup and view all the answers

What is required for the initiation of DNA synthesis?

An RNA primer synthesized by a primase Signup and view all the answers

In which direction does the synthesis of DNA occur?

From 5' to 3' Signup and view all the answers

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

It is broken. Signup and view all the answers

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

Helicase Signup and view all the answers

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

Nucleotide triphosphate substrates Signup and view all the answers

Why can DNA replication only proceed in one direction?

Because the DNA template is read from 3' to 5' Signup and view all the answers

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

Ester bond Signup and view all the answers

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

It is synthesized by a primase and later removed. Signup and view all the answers

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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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.