Lecture 1: Bacterial Genomes Flashcards
What is the traditional view of a prokaryotic genome?
Single, circular DNA molecule localized within the nucleoid
What is the nucleoid?
A lightly staining region of the cell where the circular DNA molecule in prokaryotic cells is localized.
What are the characteristics of the B form of DNA?
- 2 polynucleotide chains in opposite orientation
- Regular right handed double helix
- 2nm diameter, makes complete turn every 3.4nm
- ~10.5 bp / turn of helix
What flexibilities are present within the basic B-form of DNA?
- Numbers of base pairs per turn of the helix can be altered
- Helix in cell is not straight but coiled in 3D space
- Certain sequence features where bends occur
What are the characteristics of DNA in the B form?
- It consists of two chains in opposite orientation arranged in a right-handed double helix.
- The diameter is approximately 2 nm, and it makes a complete turn every 3.4 nm.
- There are approximately 10.5 base pairs per turn of the helix.
What is supercoiling in DNA, and how does it occur?
- Occurs when additional turns are introduced into the DNA double helix (positive supercoiling) or if turns are removed (negative supercoiling)
- In the circular genome of E. coli, DNA is supercoiled, which helps compact the DNA and regulate gene expression.
How is torsional stress accommodated in DNA molecules?
- Torsional stress in DNA molecules is accommodated in two ways:
- Formation of superhelices
- Altering the number of base pairs per turn of the helix
- These responses are expressed by the linking number (L), which represents the total number of times that the two strands of the double helix of a closed molecule cross each other when constrained to lie in a plan
What are Type I topoisomerases and how do they function?
- Type I topoisomerases break one strand of DNA, pass the other strand through the gap, and then seal the break.
- This process changes the linking number by ±1.
- An example is Topoisomerase I of E. coli, which relaxes negatively supercoiled DNA.
What is the nucleoid?
A lightly staining region of the cell where the circular DNA molecule in prokaryotic cells is localized.
What are the characteristics of the B form of DNA?
- 2 polynucleotide chains in opposite orientation
- Regular right handed double helix
- 2nm diameter, makes complete turn every 3.4nm
- ~10.5 bp / turn of helix
What flexibilities are present within the basic B-form of DNA?
- Numbers of base pairs per turn of the helix can be altered
- Helix in cell is not straight but coiled in 3D space
- Certain sequence features where bends occur
What are the characteristics of DNA in the B form?
- It consists of two chains in opposite orientation arranged in a right-handed double helix.
- The diameter is approximately 2 nm, and it makes a complete turn every 3.4 nm.
- There are approximately 10.5 base pairs per turn of the helix.
What is supercoiling in DNA, and how does it occur?
- Occurs when additional turns are introduced into the DNA double helix (positive supercoiling) or if turns are removed (negative supercoiling)
- In the circular genome of E. coli, DNA is supercoiled, which helps compact the DNA and regulate gene expression.
How is torsional stress accommodated in DNA molecules?
- Torsional stress in DNA molecules is accommodated in two ways:
- Formation of superhelices
- Altering the number of base pairs per turn of the helix
- These responses are expressed by the linking number (L), which represents the total number of times that the two strands of the double helix of a closed molecule cross each other when constrained to lie in a plan
What are Type I topoisomerases and how do they function?
- Type I topoisomerases break one strand of DNA, pass the other strand through the gap, and then seal the break.
- This process changes the linking number by ±1.
- An example is Topoisomerase I of E. coli, which relaxes negatively supercoiled DNA.
What is the function of Type I topoisomerases in DNA topology?
- Type II topoisomerases break both strands of the DNA, pass another part of the helix through the gap, and change the linking number by ±2.
- An example is DNA gyrase of E. coli, which creates negative supercoils in DNA.
What is the role of Type II topoisomerases, specifically DNA gyrase of E. coli, in DNA topology?
- Type II topoisomerases, such as DNA gyrase in E. coli, break both strands of the DNA, enabling another portion of the helix to pass through the gap, thereby altering the linking number by ±2.
- DNA gyrase is a heterotetramer composed of two subunits, A and B.
- It utilizes ATP to create negative supercoils in DNA.
- DNA gyrase plays a crucial role in DNA replication by opening up the DNA strands, facilitating processes such as unwinding and supercoiling, which are essential for DNA replication to proceed efficiently.