B-DNA Structure and Supercoiling Overview

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Questions and Answers

What type of supercoiling occurs when circular relaxed DNA is overwound?

Positive supercoil (correct)

Linear supercoil

Negative supercoil

Relaxed state

What is required for DNA supercoiling to occur?

Both strands can have nicks

DNA must be linear

At least one strand must be broken

Both strands must be intact (correct)

In which type of organism is the genome typically composed of circular DNA chromosomes?

Plants

Animals

Bacteria (correct)

Eukaryotes

Which of the following statements is true about linear DNA concerning supercoiling?

Linear DNA can form supercoils at anchored points. Signup and view all the answers

What happens when circular relaxed DNA is underwound?

It forms negative supercoil. Signup and view all the answers

What is the helical turn count of relaxed circular DNA?

One helical turn per 10.5 bp Signup and view all the answers

When describing supercoiling, which term refers to an increase in helical turns?

Positive supercoil Signup and view all the answers

Which structure is linear DNA attached to at anchored points?

Chromosome scaffold Signup and view all the answers

What primarily contributes to the diameter of the B-DNA being wider than the distance between the 1’ carbons of opposite strands?

The size of deoxyriboses and phosphates Signup and view all the answers

In which direction does over twisting occur to form positive supercoils in DNA?

Same direction as the natural helical turns Signup and view all the answers

What is the result of under twisting DNA?

Formation of negative supercoils Signup and view all the answers

How does DNA behave similarly to a coiled string?

It can form supercoils when twisted Signup and view all the answers

What is the diameter measurement of the B-DNA double helix?

About 20 Å Signup and view all the answers

What defines the term 'supercoiled' in DNA?

A form of DNA that has been twisted beyond its normal helical structure Signup and view all the answers

What role do positive supercoils play in DNA?

They compact genetic material Signup and view all the answers

What happens to the structure of DNA when it is under twisted?

It helically unwinds Signup and view all the answers

What occurs to DNA when it is underwound by one helical turn?

It negatively supercoils. Signup and view all the answers

Why is DNA usually negatively supercoiled in most cells?

It facilitates strand separation. Signup and view all the answers

What happens to DNA behind a moving transcription fork?

DNA becomes underwound and forms negative supercoils. Signup and view all the answers

What is a consequence of strand separation in DNA?

It adds a helical turn. Signup and view all the answers

What is the relationship between transcription direction and supercoiling of DNA?

Positive supercoils form ahead of the transcription fork. Signup and view all the answers

What does negatively supercoiled DNA facilitate during cellular processes?

Initiation of transcription and replication. Signup and view all the answers

What type of supercoiling is formed during strand separation in DNA?

Only positive supercoiling. Signup and view all the answers

What mechanism allows DNA to relieve strain during replication?

Negative supercoiling and strand separation. Signup and view all the answers

What does a negative value of S indicate about supercoiling in DNA?

It indicates the presence of negative supercoils. Signup and view all the answers

How is the linking number (Lk) defined in relation to supercoiling?

It indicates how many strands pass over each other. Signup and view all the answers

What is the formula for calculating supercoils (S)?

S = Lk – Lko Signup and view all the answers

In a relaxed circular DNA with 200 base pairs, what is the linking number (Lko)?

200 Signup and view all the answers

When the DNA Lk is 198 and Lko is 200, what is the value of S?

2 negative supercoils Signup and view all the answers

What characteristic is typical of DNA in most cells?

It is typically negatively supercoiled. Signup and view all the answers

If a strand of DNA has 8 helical turns, how many base pairs does it have?

84 bp Signup and view all the answers

In circular DNA, what happens when it is underwound by one helical turn?

It forms additional negative supercoils. Signup and view all the answers

Study Notes

B-DNA Structure and Dimensions

B-DNA double helix has a diameter of approximately 20 Å (angstroms).
The distance between the 1’ carbons of opposite strands is around 11 Å, but the larger diameter is due to the presence of deoxyribose and phosphate groups.
The helix has an additional width due to its structural characteristics, resulting in a "hole" in the center.

DNA Supercoiling Overview

DNA can be likened to a coiled string and can undergo supercoiling when twisted either over or under its natural helical turns.
Supercoiling can be demonstrated with a phone cord, illustrating how coiling can transition into supercoiling.

Types of Supercoiling

Positive supercoiling occurs when DNA is overwound in the same direction as the helical turns, resulting in increased tightness of the coil.
Negative supercoiling occurs when DNA is underwound in the opposite direction to the helical turns, resulting in a loosening effect.

Characteristics of Circular DNA and Supercoiling

Circular relaxed DNA manifests no supercoiling, featuring one helical turn per 10.5 base pairs (bp).
Overwound circular DNA leads to positive supercoiling, while underwound circular DNA results in negative supercoiling.
Supercoiling is contingent upon the integrity of both DNA strands; any breaks can lead to uncoiling instead of supercoiling.

Linear vs. Circular Chromosomes

Bacteria and Archaea typically possess supercoiled circular chromosomes.
Eukaryotic genomes are composed of linear DNA chromosomes, which can form supercoils between anchored points.
Linear DNA can become relaxed or supercoiled based on twisting conditions around its constrained anchors.

Linking Number and Supercoil Calculation

Linking number (Lk) indicates how many times one DNA strand winds around another.
The relaxed linking number (Lko) for relaxed DNA is calculated by dividing the total number of base pairs by 10.5.
Supercoils (S) are determined by S = Lk - Lko; a negative S indicates the presence of positive supercoils, while a positive S indicates negative supercoils.

Typical Cellular DNA State

In most cells, DNA is naturally negatively supercoiled, enhancing strand separation and facilitating DNA replication and transcription processes.
Negatively supercoiled DNA exhibits a tendency to accommodate structural strain, either through supercoiling or strand separation.

Supercoiling during Replication and Transcription

DNA strand separation during replication creates tension, leading to overwinding and the formation of positive supercoils in front of the separation fork.
Conversely, negative supercoils form behind the moving fork, resulting from underwinding.
The supercoiling dynamics are essential for efficient DNA replication and transcription, as they help relieve tension in the DNA strands.

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Description

Explore the fascinating structure of B-DNA and the principles of DNA supercoiling. This quiz covers the dimensions of the double helix, the concept of supercoiling, and the types involved. Test your understanding of how these structural characteristics impact DNA functionality.