Exam II Flashcards
chromatin
complex of DNA and proteins
what types of protein are found in chromatin?
- histones
- non-histone chromosomal proteins
chromatin consists of DNA bound to both histone and non-histone proteins. The mass of histone protein present is about equal to the total mass of non-histone protein, but—as schematically indicated here—the latter class is composed of an enormous number of different species. In total, a chromosome is about one-third DNA and two-thirds protein by mass.
What is the basic unit of eukaryotic chormosome structure?
nucleosomes
nucleosome
Each individual nucleosome core particle consists of a complex of eight histone proteins—two each H2A, H2B, H3, and H4—and double-stranded DNA that is 147 nucleotide pairs long. The histone octamer forms a protein core around which the double-stranded DNA is wound.
(The term nucleosome technically refers to a nucleosome core particle plus one of its adjacent DNA linkers, but it is often used synonymously with nucleosome core particle.)
Linker DNA
Region of DNA that seperates each nucleosome core from the next, varies from a few nucleotides to up to 80 in length.
What is the average spacing of nucleosomes on DNA
200 nucleotide pairs
What is the configuration of DNA about an individual core histone (nucleosome)?
A left-handed coil of B DNA 1.7 turns
core histones
Four: H2a, H2b, H3, H4
Small: ~ 100 amino acid residues
Basic: many lysine and arginine residues
Conserved: two amino acids different in H3 between peas and humans
Form quaternary octamer structure: two copies of each
histone fold
A histone fold is a structurally conserved motif found near the C-terminus in every core histone sequence in a histone octamer responsible for the binding of histones into heterodimers.
The histone fold averages about 70 amino acids and consists of three alpha helices connected by two short, unstructured loops. When not in the presence of DNA, the core histones assemble into head-to-tail intermediates (H3 and H4 first assemble into heterodimers then fuse two heterodimers to form a tetramer, while H2A and H2B form heterodimers) via extensive hydrophobic interactions between each histone fold domain in a “handshake motif”.
histone N-terminal tail
The tails of the cores are unstructured. They are modified to regulate the accessibility of nonhistone proteins to the DNA
In (D) of the figure below, note that all eight N-terminal tails of the histones protrude from the disc-shaped core structure. Their conformations are highly flexible, and they serve as binding sites for sets of other proteins.
What is the order of assembly of the histone octamer?
H3 and H4 bind to each other to make a dimer, and two H3-H4 dimers associate to form an H3-H4 tetramer.
Likewise, H2a and H2b form dimers, but do not form a tetramer.
DNA is wrapped around the H3- H4 tetramer.
Two H2a-H2b dimers are then added.
Note N-terminal tails always stick out
Describe the interactions between the nucelosome and DNA
The nucleosome core particle is a disk-shaped histone core (2x H2A, H2B, H3, H4) with tightly-wrapped DNA in a left-handed coil of 1.7 turns (146-147 bases per core).
Salt bridges (H-bond + electrostatics) between basic amino acid sidegroups of K/R and phosphates of DNA backbone
Additional 142 H-bonds are formed between DNA and the histone core in each nucleosome. Half of these are between the AA backbone of the histone and the _sugar-phosphate backbon_e of the DNA. Additionally, hydrophobic interactions play a role.
Minor groove is compressed substantially, this favours AA, TT, and TA dinucleotides in the minor groove due to sterics.
N-terminal tails also interact with DNA through electrostatics, controlled by protein modifiction.
The amino acids ________ and ________ together make up more than _________ of the core histone proteins.
The amino acids lysine and arginine (both have basic side chains) together make up more than 20% or 1/5 of the core histone proteins.
Their positive charges neutralise the negatively charged backbone
What dinucleotides are preferred on the minor grove of DNA bound by histone octamers?
AA, TT, and TA
Probably explains some striking, but unusual, cases of very precise positioning of nucleosomes along a stretch of DNA. However, the sequence preference of nucleosomes must be weak enough to allow other factors to dominate, inasmuch as nucleosomes can occupy any one of a number of positions relative to the DNA sequence in most chromosomal regions.
What are the two major components of a histone protein?
The histone fold that is used to bind to other histones and form di-, tri-, and octomers
The N-terminal “tail” which extends out from the DNA-histone core, subject to several types of covalent modification that control critical aspects of chromatin structure and function.
How is DNA in a nucleosome available for binding to other proteins if it is wound by histone proteins?
DNA/nucleosome “breathing”
DNA in an isolated nucleosome unwraps from each end at a rate of about four times per second, remaining exposed for 10 to 50 milliseconds before the partially unwrapped structure recloses. This allows nonhistone proteins to bind DNA.
histone H1
The “linker” histone, the H1 core region constrains an additional
20 nucleotide pairs of DNA where it exits from the nucleosome core, the angle is important for compacting chromatin.
How do histone N-terminal tails interact with DNA?
Electrostatic interactions controlled by protein modification. Additionally, tails from different cores can interact to promote additional condensation.
