What are histones and chromatin? Describe DNA packing in a nucleosome.
Eukaryotic chromosomes have linear DNA molecules associated with a large amount
of protein. Chromatin is a complex of DNA and protein and is found in the nucleus of eu-
karyotic cells. Chromatin causes condensation and organization of DNA
The protein:DNA mass ratio is 2:1 and the histone:DNA mass ratio is 1:1. Chromatin in-
cludes several levels of condensation including 10 nm fibres with nucleosomes (bead
on a string-like configuration) which offer 7x compaction. The nucleosomes are repeat
units of chromatin. This is the primary structural unit and is controlled by histones. His-
tones are the units that DNA winds around to the form the "beads".
Has a 3-helix core domain and forms a handshake like arrangement. The tails are N-ter-
minal or C-terminal that protrude from the nucleosome through minor groove channels.
They are in the ideal location for covalent modifications. It is an octamer made of up H3-
H4 tetramer and 2 H2A-H2B dimers.
Formation of the 30 nm fibers which offer 40X compaction provide the second level of
compaction. This is achieved through histone tail-mediated nucleosome-nucleosome in-
Tertiary structures are formed by tail-mediated association of individual fibres.
What positions nucleosomes and what are the functions of chromatin remod-
Nucleosomes are positioned by transcription factors, general transcriptional machinery
and chromatin remodelling ATPases. The chromatin remodelling ATPases have several
functions: transcription, repression, DNA methylation, exchange, repair and recombina-
tion. They bind nucleosomes, are DNA-dependant ATPases, recognize histone modifi-
cations, can be regulated and interact with other proteins.
What are proteosomes and what is their importance in ubiquination?
Proteosomes are giant protein complexes that bind protein molecules and degrade
them. The protein to be degraded is ubiquitinated and sent to the proteosome with this
tag to be degraded. The proteosome and the ubiquitin are recycled and the protein ends
up in fragments.
What is RNA interference? Explain roles of siRNA and miRNA mediated interfer-
Inhibition of gene expression by RNA molecules is called RNA interference (RNAi).
RNAi is caused by small interfering RNAs (siRNAs). siRNAs play a role in heterochro-
matin formation and can block large regions of a chromosome. Small RNAs can stop
transcription of a specific gene. MicroRNAs or miRNAs are small single stranded RNA
molecules that bind to mRNA and they can degrade the piece of RNA or stop it's trans-
lation. Give one example each of a positive and negative regulated operon in prokary-
Operon: A cluster of functionally related genes can be under coordinated control by a
single on-off "switch". The regulatory "switch" is a segment of DNA called an operator
usually positioned within the promoter. An operon consists of the entire stretch of DNA
that includes the operator, the promoter and the genes that they control. The operon
can be switched off a protein called a repressor. The repressor prevents gene transcrip-
tion by binding to the operator and blocking RNA polymerase. The repressor is the prod-
uct of a separate regulatory gene. The repressor can sometimes work with a co-repres-
sor. (ex. E. coli can synthesize the amino acid tryptophan, tryptophan binds to repressor
Negatively regulated operon (operons are switched off by the active form of the repres-
sor) : lac operon. It is an inducible operon and contains genes that code for enzymes
used in the hydrolysis and metabolism of lactose. The lac repressor is usually active
and switches the operon off but a