Molecular Biology: Nucleosomes and Gene Regulation

Nucleosomes are proteins that bind to and package DNA. Their primary function is to organize DNA into a compact structure, facilitating gene regulation.

Histone subunits combine in an octamer structure, consisting of two copies of H2A, H2B, H3, and H4. This structure wraps around the DNA to form the nucleosome.

Chromatin regulates gene expression by controlling access to DNA for transcription factors and RNA polymerase. It can be relaxed or compacted depending on the regulatory needs.

<p>Transcription factors, such as the helix-loop-helix heterodimer, bind to specific DNA sequences at enhancer regions. This binding facilitates the recruitment of RNA polymerase and other general transcription factors to initiate transcription.</p> Signup and view all the answers

<p>The sequence CACGTG is a specific DNA motif that transcription factors bind to in order to regulate gene expression. It is essential for the activation of genes associated with those transcription factors.</p> Signup and view all the answers

<p>The poly-Q sequence allows the clock transcription factor to interact with general transcription factors and RNA polymerase II, thereby triggering the transcription process when DNA is bent.</p> Signup and view all the answers

<p>During transcription, nucleosomes can be relaxed or modified to allow access for RNA polymerase II to move along the DNA and synthesize mRNA. This process is essential for effective gene expression.</p> Signup and view all the answers

<p>Two types of transcription factors mentioned are basic helix-loop-helix and zinc finger transcription factors. They are involved in binding to specific DNA sequences to regulate the transcription of target genes.</p> Signup and view all the answers

<p>It may prevent the activation of important genes.</p> Signup and view all the answers

<p>Barriers prevent the spread of heterochromatin into euchromatin regions.</p> Signup and view all the answers

<p>Nucleosomes are the fundamental structural units that facilitate this process.</p> Signup and view all the answers

<p>Gene-rich regions are actively transcribed, while gene-poor regions exhibit very low transcription activity.</p> Signup and view all the answers

<p>Transcription factories are areas within the nucleus where multiple genes are transcribed together.</p> Signup and view all the answers

<p>Fluorescent in situ hybridization (FISH) is used to visualize mRNA transcription.</p> Signup and view all the answers

<p>Genes from different chromosomes can co-localize in a transcription factory.</p> Signup and view all the answers

<p>These areas demonstrate dense RNA synthesis and active transcription.</p> Signup and view all the answers

<p>Transcription factories often group genes that are involved in the same pathway for coordinated expression.</p> Signup and view all the answers

<p>Gene transcription is significantly reduced or absent in anti-ridge regions.</p> Signup and view all the answers

<p>A nucleosome is formed by eight histone proteins: two copies each of H2A, H2B, H3, and H4.</p> Signup and view all the answers

<p>There are two turns of DNA wrapped around each nucleosome.</p> Signup and view all the answers

<p>The H1 histone stabilizes the nucleosome structure by binding to the outside.</p> Signup and view all the answers

<p>The chromatin fiber has a width of 30 nanometers.</p> Signup and view all the answers

<p>The core tetramer of a nucleosome is formed by two H3 and two H4 histones.</p> Signup and view all the answers

<p>Histone proteins primarily have a structure consisting of three alpha helices forming the histone fold.</p> Signup and view all the answers

<p>The histone tails are important for post-translational modifications that affect chromatin remodeling.</p> Signup and view all the answers

<p>When a cell is not dividing, the DNA becomes less highly organized.</p> Signup and view all the answers

<p>A nucleosome consists of eight histones, which ensure the proper packaging and regulation of DNA.</p> Signup and view all the answers

<p>Multiple nucleosomes stack together to form a thicker chromatin fiber.</p> Signup and view all the answers

<p>The primary reason for DNA packaging into nucleosomes is to fit all of the DNA into the nucleus.</p> Signup and view all the answers

<p>A histone protein is composed of three alpha helices connected by linkers.</p> Signup and view all the answers

<p>Histone modifications are critical because they can determine the accessibility of DNA for transcription.</p> Signup and view all the answers

<p>The phosphate backbone of DNA interacts with histones to ensure tight wrapping around nucleosomes.</p> Signup and view all the answers

<p>Acetylation relaxes histones, allowing DNA to become more accessible for transcription by RNA polymerase.</p> Signup and view all the answers

<p>HATs add acetyl groups to histones, reducing their positive charge and decreasing the binding of histones to DNA, thus promoting transcription.</p> Signup and view all the answers

<p>CLOCK functions as both a transcription factor and a HAT, facilitating DNA binding and acetylating histones to promote gene transcription.</p> Signup and view all the answers

<p>Acetylation leads to a less charged state of histones, which results in a looser chromatin structure.</p> Signup and view all the answers

<p>Hypomethylated lysine is generally associated with transcriptional activation, while hypermethylated lysine typically leads to transcriptional repression.</p> Signup and view all the answers

<p>CREB binds to the CRE, which then recruits protein 300 and CREB-binding protein.</p> Signup and view all the answers

<p>Lysine demethylases remove methyl groups from lysines, reversing hypermethylation and potentially restoring active transcription states.</p> Signup and view all the answers

<p>Hypermethylation of lysines typically represses transcription by attracting repressive protein complexes.</p> Signup and view all the answers

<p>The main histone deacetylase in humans is HDAC1, which removes acetyl groups from histones, contributing to chromatin condensation.</p> Signup and view all the answers

<p>Methylation of lysine involves adding one or more methyl groups, which alters its interaction with other proteins.</p> Signup and view all the answers

<p>The TATA binding protein helps initiate transcription by recruiting other factors and can also be involved in histone acetylation.</p> Signup and view all the answers

<p>The number of methyl groups attached to lysines determines gene activity; monomethylation usually activates while dimethylation or trimethylation can repress.</p> Signup and view all the answers

<p>DNA bending facilitates the recruitment of transcription factors and the formation of a transcriptional complex.</p> Signup and view all the answers

<p>Histone tails can undergo modifications like acetylation, methylation, phosphorylation, and ubiquitination, which influence gene expression by either activating or repressing transcription.</p> Signup and view all the answers

<p>Lysine acetylation generally promotes transcription by modifying the chromatin structure to allow easier access for transcription factors.</p> Signup and view all the answers

<p>Chromatin remodeling enzymes shift histones to make binding sites more accessible to transcription factors or to hide them, thereby facilitating or inhibiting transcription.</p> Signup and view all the answers

<p>The FACT protein shuttles histones away from the DNA, allowing RNA polymerase II to transcribe past them and then reassembles the histones afterward.</p> Signup and view all the answers

<p>Insulators and barriers prevent adjacent DNA from interacting, thereby regulating the expression of genes by blocking unwanted activation or repression.</p> Signup and view all the answers

<p>Methylation of lysines and arginines can lead to either gene activation or repression, depending on the specific context and combinations of modifications present.</p> Signup and view all the answers

<p>The epigenetic histone code refers to the combination of post-translational modifications of histones that dictate the transcriptional activity of associated genes.</p> Signup and view all the answers

<p>Serine, threonine, and tyrosine are the amino acids commonly phosphorylated during histone modification.</p> Signup and view all the answers

<p>Acetylation alters chromatin structure to make it more open and accessible for transcription factors and RNA polymerase.</p> Signup and view all the answers

<p>A lysine residue on a histone tail can be either acetylated or methylated, leading to distinct effects on transcriptional regulation.</p> Signup and view all the answers

<p>Higher order domains refer to the spatial arrangement of chromatin that influences gene expression and transcription efficiency.</p> Signup and view all the answers

<p>Transcription factories are multi-subunit complexes where active transcription occurs, bringing together various transcriptional machinery.</p> Signup and view all the answers

<p>Understanding which histone is being modified is crucial for interpreting the functional significance of the modification on gene regulation.</p> Signup and view all the answers

<p>Processes such as mitosis, meiosis, DNA replication, DNA repair, apoptosis, and transcription are influenced by post-translational histone modifications.</p> Signup and view all the answers

<p>Remodelling complexes modify histone positioning to make important DNA binding sequences more accessible for transcription.</p> Signup and view all the answers

<p>FACT removes H2A and H2B dimers to allow RNA polymerase access to DNA and then reassembles the histones after transcription.</p> Signup and view all the answers

<p>They contact other proteins to facilitate the recruitment of a functional transcription pre-initiation complex, triggering RNA polymerase to start transcribing.</p> Signup and view all the answers

<p>Locus control regions can activate multiple genes and operate over much longer distances, typically 30 to 100 kilobases away from the genes they regulate.</p> Signup and view all the answers

<p>Insulators create boundaries that prevent enhancers from activating adjacent genes, ensuring specific regulation of transcription.</p> Signup and view all the answers

<p>Enhancers interact with transcription factors to organize protein complexes that facilitate the transcription of target genes.</p> Signup and view all the answers

<p>Common types include proline-rich, glutamine-rich, and acidic-rich activation domains.</p> Signup and view all the answers

<p>Histone modifications, such as acetylation, can either promote or inhibit the accessibility of DNA, influencing transcription.</p> Signup and view all the answers

<p>Barriers function to separate euchromatin from heterochromatin, maintaining the integrity of transcriptionally active and inactive regions.</p> Signup and view all the answers

<p>During transcriptional elongation, RNA polymerase must navigate through nucleosomes, requiring dynamic changes in histone positioning.</p> Signup and view all the answers

<p>Activators work at a distance to bring various regulatory proteins into proximity at the promoter, which is essential for initiating transcription.</p> Signup and view all the answers

<p>Histone acetyltransferases add acetyl groups to histones, reducing their positive charge and decreasing the binding affinity for DNA, leading to increased accessibility.</p> Signup and view all the answers

<p>After the polymerase moves past, FACT helps reassemble the histones to restore the chromatin structure.</p> Signup and view all the answers

<p>Euchromatin is transcriptionally active and loosely packed, while heterochromatin is transcriptionally inactive and tightly packed.</p> Signup and view all the answers

<p>They catalyze the transfer of methyl groups from S-adenosylmethionine to arginine residues on histones, influencing gene activation.</p> Signup and view all the answers

<p>Asymmetric dimethylation occurs when the same nitrogen is methylated twice, while symmetric dimethylation involves methylation on different nitrogen atoms.</p> Signup and view all the answers

<p>It primarily methylates histone 4 at arginine 3, which is associated with transcriptional activation.</p> Signup and view all the answers

<p>Histone acetylation generally opens up chromatin structure, promoting transcriptional activation.</p> Signup and view all the answers

<p>Hypermethylated histones are typically associated with gene repression.</p> Signup and view all the answers

<p>Histone 3 lysine 9 is hypomethylated in the active state.</p> Signup and view all the answers

<p>Different modifications act as markers that attract or repel regulatory proteins, affecting transcription.</p> Signup and view all the answers

<p>They reposition histones along DNA to expose or conceal important regulatory regions necessary for transcription.</p> Signup and view all the answers

<p>SWI-SNF is an ATP-dependent chromatin remodeling complex that facilitates histone sliding to open or close DNA regions.</p> Signup and view all the answers

<p>Methylation of H3K9 is associated with transcriptional repression.</p> Signup and view all the answers

<p>Acetylation of lysines, particularly H4 lysine 16, helps recruit proteins that facilitate transcription.</p> Signup and view all the answers

<p>Bromodomain proteins bind to acetylated lysines, promoting transcriptional activation.</p> Signup and view all the answers

<p>When a gene is wrapped in histones, it becomes less accessible, inhibiting transcription.</p> Signup and view all the answers

<p>Active genes are typically marked by acetylated histones, while repressed genes show hypermethylation.</p> Signup and view all the answers

<p>Acetylation loosens chromatin structure for transcription, while deacetylation tightens it, often leading to repression.</p> Signup and view all the answers

Proteins that bind to and package DNA, forming the fundamental unit of chromatin.

A complex of DNA wrapped around a core of histone proteins.

Proteins that form the core of the nucleosome, acting as 'spool' for DNA.

The state of DNA and its associated proteins within the nucleus.

DNA wrapped around histone proteins.

A compact and tightly packed form of chromatin.

A less condensed form of chromatin, allowing for gene expression.

The process of converting euchromatin into heterochromatin, regulating gene expression.

Nucleosomes are the basic unit of DNA packaging, consisting of a core of eight histone proteins (two copies of each histone H2A, H2B, H3, and H4) around which two turns of DNA are wrapped.

The H1 histone helps stabilize the nucleosome structure by binding to the linker DNA region between two nucleosomes.

Nucleosomes are packed into a 30nm fiber, creating a more compact structure.

The histone fold domain, located in the middle of each histone protein, mediates the interaction between histones.

The core tetramer of a nucleosome is formed by two H3 and two H4 histones.

The H2A and H2B histones associate with the core tetramer to complete the nucleosome structure.

The DNA wraps around the histone core through interactions with the phosphate backbone.

Histone tails extend from the nucleosome and are subject to various modifications, which play a crucial role in regulating gene expression.

The process of DNA packaging starts with nucleosome assembly, followed by further condensation into 30nm fibers and eventually into chromosomes.

Chromosomes are only present during cell division, whereas during other phases of the cell cycle, DNA is less tightly organized.

The histone fold domain is composed of three alpha helices linked by short loops.

Histone modifications, such as acetylation, methylation, and phosphorylation, alter the accessibility of DNA and affect gene expression.

Chromatin remodeling refers to the dynamic process of altering chromatin structure, allowing access to DNA for transcription.

Nucleosomes are essential for packaging DNA within the nucleus, allowing large amounts of genetic material to fit into a compact space.

The modifications that occur on histone tails can influence whether a gene is transcribed.

A type of post-translational modification that occurs on histone tails, involving the attachment of an acetyl group (COCH3) to a lysine residue.

Enzymes that add acetyl groups to lysine residues on histone tails, promoting gene activation by relaxing chromatin structure.

Enzymes that remove acetyl groups from lysine residues on histone tails, leading to gene repression by tightening chromatin structure.

A type of post-translational modification that occurs on histone tails, involving the attachment of a methyl group (CH3) to either a lysine or arginine residue.

Methylation of lysine or arginine residues on histone tails can either activate or repress gene expression, depending on the specific amino acid and the number of methyl groups attached.

Enzymes that add methyl groups to lysine or arginine residues on histone tails.

Enzymes that remove methyl groups from lysine or arginine residues on histone tails.

A complex of proteins that can reposition nucleosomes along DNA, making DNA more or less accessible for transcription.

A protein complex that temporarily removes histones from DNA, allowing RNA polymerase II to pass through and transcribe genes.

DNA sequences that act as insulators, blocking the spread of regulatory elements from one gene to another.

DNA sequences that act as barriers, preventing the spread of heterochromatin from one chromosomal region to another.

Specific regions within DNA that control the expression of multiple genes in a linked domain, often by promoting an open chromatin state.

Regions of chromosomes that are organized into functional units, often involving specific compartments within the nucleus.

Specialized nuclear compartments where genes are actively transcribed, often containing multiple RNA polymerases and associated proteins.

A chemical modification that adds an acetyl group (CH3CO) to the lysine residues in histone tails.

The state of chromatin where histone tails are acetylated, leading to a more relaxed and accessible DNA structure.

The state of chromatin where histone tails are not acetylated, leading to a more condensed and less accessible DNA structure.

A chemical modification that adds a methyl group (CH3) to the lysine residues in histone tails.

Enzymes that catalyze the addition of methyl groups to lysine residues in histone tails.

Enzymes that remove methyl groups from lysine residues in histone tails.

The state of histone lysine methylation with one methyl group, often associated with gene activation.

The state of histone lysine methylation with two methyl groups, often associated with gene activation.

The state of histone lysine methylation with three methyl groups, often associated with gene repression.

A DNA sequence that binds to specific transcription factors, leading to the activation of gene expression.

A protein that binds to a specific DNA sequence (enhancer element) and activates gene expression.

A complex of proteins that bind to activators and facilitate chromatin remodeling and transcription.

A protein that binds to the promoter region of a gene and recruits RNA polymerase for transcription.

A specialized region of DNA where heterochromatin stops spreading, preventing it from silencing important genes.

The process of DNA packaging into highly condensed structures that are visible during cell division.

A type of chromatin where genes are densely packed and inactive, preventing gene expression.

Regions of DNA where genes are loosely packed and active, facilitating gene expression.

A protein that methylates arginine residues on histone tails, often associated with gene activation.

A specific type of PRMT that methylates histone H4 at arginine 3, generally contributing to gene activation.

A specific type of PRMT that methylates histone H3 at arginine 17, also activating transcription indirectly by activating the acetylase complex.

A type of histone modification involving the addition of a methyl group to arginine residues, often associated with gene activation.

The state where a gene is being actively transcribed.

The state where a gene is prevented from being transcribed.

A region within a gene where transcription factors bind to initiate gene expression.

A region within a gene containing the coding sequences for a protein.

Specialized protein complexes that remodel chromatin structure by repositioning nucleosomes, allowing access to specific DNA regions.

A specific type of chromatin remodeling complex that uses ATP to slide nucleosomes along the DNA.

A specific type of chromatin remodeling complex that contains histone acetylation and deacetylation activities.

A specific type of chromatin remodeling complex that contains histone acetylation and deacetylation activities.

A specific type of chromatin modification that involves the addition of a methyl group to lysine residues on histone tails, often associated with gene repression.

Chromatin remodelling complexes can alter the accessibility of DNA sequences for transcription, shifting histones to either reveal or conceal regulatory elements.

FACT (Facilitator of Active Chromatin Transcription) is a protein complex that temporarily disassembles histones ahead of RNA polymerase II, allowing the polymerase to transcribe the DNA. After the polymerase has passed, FACT reassembles the histones.

Enhancer elements, often located far from the gene they regulate, contain specific DNA sequences that can bind to transcription factors with histone acetyltransferase activity, promoting the recruitment of RNA polymerase and transcription initiation.

Transcriptional activation domains are regions within activator proteins that bind to other proteins, facilitating the assembly of a functional transcription pre-initiation complex at the promoter.

Three common types of activation domains found in activator proteins are proline-rich, glutamine-rich, and acidic-rich.

Locus control regions (LCRs) are DNA elements that act like powerful enhancers, regulating gene expression at a much larger distance, often controlling several genes in tandem.

Insulators are DNA sequences that act as boundaries, preventing enhancer elements from influencing genes in adjacent regions. Insulators are crucial for maintaining proper gene expression by creating ‘transcriptional domains’.

Barriers are similar to insulators, but they specifically demarcate the boundary between euchromatin (active genes) and heterochromatin (inactive genes).

Euchromatin is a less condensed form of chromatin that is accessible for transcription, allowing genes in this region to be expressed. Euchromatin is generally located in areas of the nucleus where active gene expression is taking place.

Heterochromatin is a tightly packed form of chromatin that is inaccessible for transcription. It is typically found in regions like telomeres (chromosome ends) and near the centromere, where gene expression is generally repressed.

Histones are proteins that form the core of nucleosomes, acting like spools around which DNA is wrapped. Histones play a crucial role in packaging DNA and regulating gene expression.

Nucleosomes are the fundamental unit of chromatin, consisting of DNA wrapped around a core of eight histone proteins. They act like beads on a string, packaging DNA into a compact form within the nucleus.

Chromatin is the complex of DNA and associated proteins found within the nucleus of eukaryotic cells. It is essential for packaging DNA, controlling gene expression, and protecting the DNA from damage.

Transcriptional elongation is the process by which RNA polymerase moves along the DNA template, extending the growing RNA transcript. This process is crucial for synthesizing RNA molecules that carry genetic information.

The core promoter is a DNA region located upstream of the gene's transcription start site, containing elements that are essential for binding of RNA polymerase II and initiating transcription. The TATA box is a key component of the core promoter.