17+18

Describe a reversible histone covalent modification reaction, the amino acid modified and the enzymes and coenzymes involved?

...

Describe 3 different covalent modifications that occur on lysine residues of histones.

Acetylation Methylation Phosphorylation

What makes nucleosomes sometimes position on DNA in a non-random way?

Certain regions contain positioned nucleosomes, while others move - (these are random)

How are the general structural characteristics of chromatin thought to be different in transcribed versus non-transcribed chromosomal regions?

Changes in covalent modifications of core histones Changes in positioning of nucleosomes along the 10nm fiber Histone H1 less tightly bound Presence of HMG DNA binding proteins Variant H2A within nucleosomes in the promoter region of genes that are active, is thought to facilitate nucleosome disruption at gene promoters

What is chromatin, euchromatin, and heterochromatin?

Chromatin - composed of DNA and Histone proteins but also of non-histone proteins Euchromatin - transcribed genes (also genes ready to be transcribed) are less compact Heterochromatin - never transcribed genes (in a specific cell type) and centromeric and telomeric DNA regions (in all cells) are highly condensed/compacted into high order chromatin structures

What are the changes in chromatin structure that occur within actively transcribed DNA regions?

Chromatin looser - tails/histones are not tightly bounded

Which covalent histone modification often occurs at actively transcribed genomic loci and why?

Chromatin modifying cofactor (e.g. HAT) recruited by DNA bound activator

What are the 2 global steps in transcription activation of genes within chromatin?

Chromatin unfolding via covalent modifications of histones and nucleosome remodeling Recruitment of transcription machinery to promoters & RNA synthesis/transcription

What are core histones and what do they form the core of?

Core: H2A, H2B, H3, H4 Forms core of octamer of nucleosome core particle

What are HMG proteins?

High Mobility Group DNA binding proteins Function as architectural proteins by inducing specific DNA and nucleosome conformations that favor cooperative DNA-binding by transcription factors

Why (and how) does the degree of chromatin compaction affect transcription of genes?

Highly compacted genes are not transcripted often because they need to be loosened up so that it can be transcribed. Therefore, chromatins that are not highly compacted are usually more highly transcripted.

What are the 2 general classes of enzymes that modify chromatin structure?

Histone-modifying enzymes Add (or remove) covalent groups on histones ATP-dependent nucleosome remodeling enzymes Uses the energy of ATP hydrolysis to assemble disassemble, or slide/move nucleosome along DNA.

What are histones? Name and describe them and their role in the cell.

Histones are the proteins closely associated with DNA molecules. They are responsible for the structure of chromatin and play important roles in the regulation of gene expression. H1 - binds the outside of core nucleosomes and further compacts DNA Linker histone H1- stabilises the 30 nm fiber

What is a linker histone and what is its role?

Linker histone is H1 the role is to join a histone together- stabilises the 30 nm fiber

What is the 10nm fiber? Describe its repeating units and how much DNA is in each unit.

Loops decondense to 10 nm fibers in transcribed regions Beads on a string - comprised of repeating nucleosome (?) with 160-200bp

Describe the structure of a nucleosome and a nucleosome core particle.

Nucleosome - basic structural repeating unit of chromatin and is the first level of order in chromatin. The nucleosome is composed of DNA, 2 copies each of 4 core histones, and one linker histone

What is the purpose of nucleosomes?

Nucleosomes are made up of DNA wrapped around histone complexes in a pattern that is universal in eukaryotic cells. They apparently function to reduce the overall length of DNA in the nucleus, thus helping to keep the chromatin organized.

How does histone tail acetylation influence chromatin condensation?

Tails are bound by regulators that have a histone code recognition domain. Parental histones segregate randomly to the nascent chromatids and carry the histone bound regulators along.

What is the 30nm fiber? Describe its structure.

comprised of two-start helix of chains of nucleosomes The 30nm fiber further folds into loop regions that remain attached to a nuclear protein scaffold. Genes are primarily located in the loops

Are histones found in prokaryotes or eukaryotes?

euk

What is the role of histone H1 in chromosomes structure?

linker

What modifications of histones have a functional role in gene transcription?

regulation

Besides gene transcription, are there other DNA processes influenced by chromatin structure?

yes