Genome Organisation Flashcards
What is positive super coiling?
DNA overrotated
Helix twists on itself
What are the four possible nitrogenous bases for DNA?
Adenine
Thymine
Cytosine
Guanine
What are the four possible nitrogenous bases for DNA?
Adenine
Thymine
Cytosine
Guanine
Why are Adenine and Guanine called purines?
have double rings
Why are Thymine and Cytosine called pyrimidines?
Only one ring
What is the approximate amount of base pairs for each turn in the helix of DNA?
10
What does the major groove contain?
base pair specific information
What does the minor groove contain?
base pair non specific information
What are the two main ways for viral genome packaging?
Many viruses assemble their capsids around the viral genomes
form protein capsid shells first and then package their genomes into the procapsids
How does ssRNA helical tobacco mosaic virus package its genome?
assemble capsid around genome
How do some dsRNA and dsDNA viruses package their genome?
some dsDNA viruses (like herpesviruses) and dsRNA viruses (e.g. φ6 and φ12 bacteriophages) form protein capsid shells first and then package their genomes into the procapsids. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space.
What is the typical bacterial genome like?
typically comprised one circular chromosome but often harbored extrachromosomal elements in the form of plasmids or phages
How does the bacterial genome form nucleoids?
genome interacts with proteins (nucleoid-associated proteins H-NS and HU) and is tightly negatively supercoiled
What is Topoisomerase?
The enzyme responsible for adding and removing turns in the coil
When does positive supercoiling occur?
DNA overrotated so it twists on itself
When does negative supercoiling occur?
DNA underrotated
twists on itself in the opposite direction
How does topoisomerase I catalyse relaxation of negative supercoils
(1) cleavage of one DNA strand;
(2) passage of a segment of DNA through the break, and
(3) resealing the break. No ATP energy required for this reaction.
How does topoisomerase I catalyse relaxation of negative supercoils
(1) cleavage of one DNA strand;
(2) passage of a segment of DNA through the break, and
(3) resealing the break. No ATP energy required for this reaction.
What is the Hierarchical organization of the eukaryotic genomic DNA
double stranded DNA helix
nucleosome
30nm chromatin fiber
What is the subunit of chromosomes?
chromatin
What is chromatin made of?
nucleosome
What is euchromatin?
undergo condensation and decondensation in the cell cycle
What is heterochromatin?
remains tightly condensed throughout the cell cycle
What is a nucleosomes?
The nucleosome is a cylinder with DNA organized into ~1.7 turns around the surface.
Nucleosome looks like beads on a string in the chromatin
Nucleosomes contain an octamer of histones around which DNA winds up
Makes chromatin
What is the length of DNA in a nucleosome (in base pairs and histones)?
146bp - 260bp
histones
In base pairs how long is the core DNA?
146bp
What is Histone H1 for?
H1 is associated with linker DNA and can lie at the point where DNA enters or exits the nucleosome.
What Histones is a nucleosome made of?
2 x H2A
2 x H2B
2 x H3
2 x H4
What does the linker DNA region disfavour?
nucleosome formation
by
exhibiting a strong preference for sequences that resisting DNA bending
What does the linker DNA region disfavour?
nucleosome formation
by
exhibiting a strong preference for sequences that resisting DNA bending
What does a Nucleosome core particle (NCP) contain?
8 histones and 146-147 bp of DNA wrapped around it in ~1.7 left-handed super helical turns
What is the linker histone?
H1 variants
H1 interacts with the NCPs and linker DNA to facilitate formation of higher order chromatin structures.
What connects linker DNA?
NCPs are connected by linker DNA strands and a linker histone H1. H1 interacts with the NCPs and linker DNA to facilitate formation of higher order chromatin structures.
What are chromatosomes
Chromatosomes are nucleosomes that contain linker histones
What is the structural motif of the core histones?
consists of two short helices flanking a longer alpha-helix. This is important for the dimerization of histones and it contributes to the “globular core” of the nucleosomes.
What is the structural motif of the core histones?
consists of two short helices flanking a longer alpha-helix. This is important for the dimerization of histones and it contributes to the “globular core” of the nucleosomes.
What do flexible histone tails contain?
Flexible histone tails projecting out of nucleosome core contain sites for covalent modifications
What do flexible histone tails contain?
Flexible histone tails projecting out of nucleosome core contain sites for covalent modifications
Core histones have a flexible tail. explain
Each core histones have a flexible N-terminal tail and H2A and H2B also have a flexible C-terminal tail. The N- and C-terminal histone tails extend out of the nucleosome core structure and it is free of DNA.
How can Histones can be reversibly covalently modified on their tails?
methylation, acetylation, phosphorylation, ubiquitylation, sumoylation, ADP-ribosylation
What is the histone code?
epigenetic marking system using different combinations of histone modification patterns to regulate specific and distinct functional outputs of eukaryotic genomes. Histone code is used as an analogue expression to genetic code.
What are the PTM writers?
Histone acetyl transferase
Histone methyl transferase
Ubiquitin ligase
How does chromatin structure regulates expression?
The packaging of DNA into chromatin plays a crucial role in regulating its accessibility for RNA polymerases and transcription factors.
The level of chromatin condensation is dependent on the differentiation state of a cell, ranging from a hyper-dynamic, highly accessible structure in embryonic stem cells to a less accessible more condensed form in senescent cells.
The posttranslational modification of histones can alter the properties of chromatin fibers and is therefore a prime candidate to mediate the stable inheritance of chromatin structures.
How does chromatin structure regulates expression?
The packaging of DNA into chromatin plays a crucial role in regulating its accessibility for RNA polymerases and transcription factors.
The level of chromatin condensation is dependent on the differentiation state of a cell, ranging from a hyper-dynamic, highly accessible structure in embryonic stem cells to a less accessible more condensed form in senescent cells.
The posttranslational modification of histones can alter the properties of chromatin fibers and is therefore a prime candidate to mediate the stable inheritance of chromatin structures.
What are the roles of histone modification?
Structural changes of chromatin (regulating chromatin condensation and DNA accessibility):
Replication
Transcription (activation/repression)
Histone deposition on DNA
Recombination
DNA repair
DNA methylation
