Biology Chapter on DNA Structure and Function

DNA supercoiling is a form of DNA structure where the DNA double helix is twisted upon itself. This occurs when the DNA molecule is overwound or underwound relative to its relaxed state.

Positive supercoiling occurs when DNA is overwound. This results in a more compact structure that can be beneficial in certain environments.

Negative supercoiling occurs when DNA is underwound. This results in a more relaxed structure that makes it easier for DNA to be unwound and transcribed.

Topoisomerases are enzymes that can change the supercoiling state of DNA. They play a crucial role in DNA replication, transcription, and repair.

Chromatin is the complex of DNA and proteins that makes up chromosomes. It's organized into a hierarchical structure, starting with nucleosomes and extending to higher-order structures.

Nucleosomes are the basic repeating unit of chromatin. They consist of a core of eight histone proteins around which a length of DNA is wrapped.

Histone variants are different versions of the core histone proteins that can affect chromatin structure and gene expression. They can influence the way DNA is packaged and accessed.

Histone modifications are chemical changes to histone proteins, such as acetylation or methylation. These modifications can affect the accessibility of DNA to regulatory proteins, influencing gene expression.

Most cellular DNA is underwound, meaning it has fewer turns than the relaxed B-form structure. This underwinding facilitates DNA packaging and access to genetic information.

The process of changing the number of turns in a DNA molecule by transiently breaking and rejoining DNA strands. This alters the supercoiling state of DNA.

A circular DNA molecule with no supercoiling.

DNA molecules that are twisted or coiled upon themselves, having more or fewer turns than the relaxed B-form structure.

Enzymes that catalyze the underwinding and relaxation of DNA by breaking and rejoining DNA strands. They play an important role in replication, transcription, and DNA packaging.

Topoisomerases that break one DNA strand, pass the unbroken strand through the break, and then re-ligate the broken ends. This changes the linking number by ±1.

Topoisomerases that break both DNA strands, pass one segment through the break, and then re-ligate the broken ends. This changes the linking number by ±2.

The number of times one strand of DNA winds around the other in a closed circular DNA molecule.

DNA Gyrase is a bacterial topoisomerase that introduces negative supercoiling into circular bacterial DNA. This compaction helps with DNA replication and transcription.

Eukaryotic DNA is underwound, meaning it has fewer turns in the helix than relaxed DNA. This underwinding is achieved through chromatin assembly and topoisomerase activity.

Nucleosome formation, where DNA wraps around histone cores, induces negative supercoiling in DNA. This is due to the DNA bending around the histones.

Topoisomerases can relax positive supercoils that arise during chromatin assembly, further contributing to the overall negative supercoiling of eukaryotic DNA.

Chromosomes are highly compacted structures of DNA and proteins. This compaction allows for efficient packaging of the genetic material within the cell nucleus.

Eukaryotic chromosomes undergo significant structural changes during the cell cycle. They condense during mitosis and decondense during interphase, allowing for both DNA replication and cell division.

A long, double-stranded, circular DNA molecule that makes up the genetic material of bacteria. Contains all the genes required for bacterial function.

Small, circular DNA molecules found in bacteria, separate from the main bacterial chromosome. Often carry genes that provide bacteria with extra abilities, like antibiotic resistance.

A region within a bacterium where the bacterial chromosome is located.

A protein scaffold that helps organize the bacterial chromosome into looped domains. It plays a role in DNA compaction and regulation.

Segments of the bacterial chromosome that are physically separated from each other and are topologically constrained. These loops are about 10,000 base pairs long.

The fundamental organizational unit of chromatin, consisting of a core of eight histone proteins around which a length of DNA is wrapped.

The DNA that connects two adjacent nucleosomes.

A histone protein that binds to linker DNA, contributing to the packaging of chromatin.

Small, basic proteins that play a crucial role in packaging DNA into chromatin. They are highly conserved across eukaryotes.

The interaction between histones and DNA primarily involves the conserved histone fold and the DNA's sugar-phosphate backbone and minor groove.

The unstructured regions at the N- and C-termini of histone proteins, which can be modified to regulate gene expression.

The core of a nucleosome consists of two copies each of four histone proteins: H2A, H2B, H3, and H4.

The process of DNA wrapping around histone proteins to form nucleosomes, ultimately leading to the packaging of DNA into chromatin.

The "beads-on-a-string" structure refers to the way nucleosomes are linked together by DNA, forming a chain-like structure.

SMC proteins are a family of non-histone proteins involved in the structural maintenance of chromosomes. They play a crucial role in DNA replication and repair.

Transcription factors (TFs) are proteins that regulate gene expression. They bind to DNA and either promote or repress the transcription of specific genes.

Nonspecific nucleases like micrococcal nuclease (MNase) can cut DNA where it is not associated with proteins. This allows us to study the organization of DNA in chromatin.

The DNA in chromosomes undergoes progressive levels of organization, from nucleosomes to higher-order structures, to achieve a high degree of compaction. This organization is essential for fitting the entire genome into the nucleus of a cell.

Roger Kornberg won the Nobel Prize in Chemistry in 2006 for his groundbreaking work on the molecular basis of eukaryotic transcription.