Chromatin Flashcards
what is the packaging of DNA?
- the condensed state of the DNA is the result of interactions with basic proteins
- high density
- packaged with positively charged proteins to enable supercoiling the negative phosphodiester backbone in DNA
- means no transcription is occurring
what is the density of DNA in bacteria? in eukaryotic nucleus? in T4 phages?
- bacteria = 10 mg/mL
- eukaryotes = 100 mg/mL
- T4 = 500 mg/mL
what does packaging relate to?
- expression
- condensed means there is no transcription
packaging ratios
- length of DNA divided by the length of the unit that contains it
- unpackaged DNA to packaged DNA
- lower the ratio the less active transcription is occurring
what is the packaging ratio of interphase chromatin?
1,000 - 2,000
what is the packaging ratio of mitosis?
5,000 - 10,000
how do you calculate packaging ratios?
- 46,000,000 bp = 14 um unpackage v 2 um packaged
- 14,000 / 2 = 7,000 packaging ratio
what is DNA density?
- mass of DNA per volume
- for example, bacteria has a DNA density of 10 mg/mL
what are the different types of genomes?
- virus = TMV, phage fd and T4, and adenovirus
- prokaryote = e. coli
- eukaryote = mitochondria and nucleus
what is the length of the human genome compared to the bacterial genome?
- humans = 1.8 m (5.9 ft) / 6 x106 kb
- bacteria = 1.3 m (4.2 ft) / 4.2x103 kb
what are the types of viral packaging and what viruses are they associated with?
- filamentous = TMV and phage fd
- icosadedron = adenovirus and phage T4
what is the bacterial genome?
- 80% DNA by mass
- unfolded by agents that act on RNA or proteins
- condensing proteins are not completely understood
how is bacterial genome organized?
- independent domains or loops that contain 40 bp per loop
- genome is supercoiled and organized into loops
- nucleoid has 100 independent negatively charged super coiled domains
- 1 super coil contains 100 bp
- each loop contains 10 - 40 bases
supercoiling density
- 1 supercoil per 100 bp
- 100 loops of fibers per genome
- enough to influence melting of DNA promoters
what proteins are involved in DNA binding in bacteria?
- HU, IHF, H1, and protein P
HU
dimer that condenses DNA into bead-like structure
IHF
integration host factor
H1
interacts with bent DNA
- not the same H1 in eukaryotes
protein P
resembles protamine (found in sperm); very basic
what is the eukaryotic genome comprised of?
- 50% DNA
- 10% RNA
- the rest is proteins, with half of the proteins histones
how is the eukaryotic genome organized?
- loops of DNA about 60 kb but can range from 20-200
- composed of scaffold proteins
MAR
- matrix attachment region
- DNA binds to nuclear matrix within nuclear membrane
- appear to be associated with scaffold proteins
- heterochromatin is strongly associated here
euchromatin
- much less densely packed and dispersed
- only small portion transcribed
- more likely to be transcribed, does not mean it will be
heterochromatin
- inactive
- two kinds: facultative and constitutive
constitutive heterochromatin
- regions that are not expressed, remain condensed
- structural and remain near centromeres
facultative heterochromatin
- entire chromosomes that are inactive in one cell lineage in the female
- mosaic in cells, one cell can have a different active X chromosome than another
what are the 10, 30, and 50 nm fibers?
- 10 nm = beads on a string
- 30 nm = compact beads on a string
why is the beads on a string model no longer accurate past the 30 nm fiber?
- based on the hierarchal model that is no longer accurate because is only present in isolated DNA and does not occur naturally
- beads on a string are all packaged at different densities and not that organized
explain scaffolding
- the mitotic chromosome is comprised of consecutive loops formed by condensin 1 and 2
- mega loops nested within smaller loops all situated on a backbone
- condensin 2 forms the primary loops while condensin 1 forms sub-loops
- first structure wraps around over and over with other to form a large structure
condensin 1
within primary loops to form subloops
condensin 2
- spirals that form the central structure of the condensed chromosome
lampbrush chromosomes
- highly extended conformation at 400 - 800 um (normal is 15-20)
- found in amphibians like newt and frog
- have extended meiosis for several months
- found within normal DNA with loops that are heavily transcribed
- contains ribonucleoproteins
polytene chromosomes
- drosophila larval salivary glands interphase nuclei
- more than 5,000 bands with a packaging ration more than 20
- comprised of parallel fibers running longitudly that result in the chromosome doubling up to 9 times
- transcriptionally active bands are puffed forming balbiani rings
what occurs in puff and balbiani rings?
intense RNA synthesis
- can tell the order based on short to long
what is a centriole?
- involved in the development of spindle fibers for cell division
- not found in all organisms
what is a centrosome?
- eukaryotic segregation device
- no DNA sequence but epigenetic modifications
what are MTOCs?
- microtubular organizing center
- found at centrioles at the poles and on each chromosome at the center
what is a kinetochore?
- 400 nm fiber found at centromere that is attached to the microtubules during mitosis
- provides MTOC for chromosome
what is the unusual yeast kinetochore?
Dam 1
budding yeast centromere structure
point centromere
insects, mammals, and plant centromere structure
regional centromeres
nematodes centromere structure
holocentric chromosome
regional chromosomes
- contain a centromere specific histone H3 variant and repetitive DNA
- alternating pattern of H3 octamers and CenH3 tetrameres
- the Cen H3 tetramers recruit proteins that form the kinetochore
- location seems to be epigenetically controlled
why is the regional centromere more beneficial over the point centromere?
the point centromere can only accommodate a single turn of DNA
chromatin
a complex chiefly of DNA and histone in eukaryotic cells that is usually dispersed in the interphase nucleus and condensed into chromosomes in mitosis and meiosis
interphase nucleus
no condensed chromosomes
- chromosomes occupy specific territories within the nucleus and are not entangled
acentric fragment
does not get attached to mitotic spindle
