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Anatomy and Cell Biology
Anatomy and Cell Biology 4411B

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". Histone structure: 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- teractions. Tertiary structures are formed by tail-mediated association of individual fibres. What positions nucleosomes and what are the functions of chromatin remod- elling ATPases? 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- ence mechanisms. 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- otes. 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 when produced). 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
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