Chromatin Flashcards
1
Q
what is the packaging of DNA?
A
- 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
2
Q
what is the density of DNA in bacteria? in eukaryotic nucleus? in T4 phages?
A
- bacteria = 10 mg/mL
- eukaryotes = 100 mg/mL
- T4 = 500 mg/mL
3
Q
what does packaging relate to?
A
- expression
- condensed means there is no transcription
4
Q
packaging ratios
A
- 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
5
Q
what is the packaging ratio of interphase chromatin?
A
1,000 - 2,000
6
Q
what is the packaging ratio of mitosis?
A
5,000 - 10,000
7
Q
how do you calculate packaging ratios?
A
- 46,000,000 bp = 14 um unpackage v 2 um packaged
- 14,000 / 2 = 7,000 packaging ratio
8
Q
what is DNA density?
A
- mass of DNA per volume
- for example, bacteria has a DNA density of 10 mg/mL
9
Q
what are the different types of genomes?
A
- virus = TMV, phage fd and T4, and adenovirus
- prokaryote = e. coli
- eukaryote = mitochondria and nucleus
10
Q
what is the length of the human genome compared to the bacterial genome?
A
- humans = 1.8 m (5.9 ft) / 6 x106 kb
- bacteria = 1.3 m (4.2 ft) / 4.2x103 kb
11
Q
what are the types of viral packaging and what viruses are they associated with?
A
- filamentous = TMV and phage fd
- icosadedron = adenovirus and phage T4
12
Q
what is the bacterial genome?
A
- 80% DNA by mass
- unfolded by agents that act on RNA or proteins
- condensing proteins are not completely understood
13
Q
how is bacterial genome organized?
A
- 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
14
Q
supercoiling density
A
- 1 supercoil per 100 bp
- 100 loops of fibers per genome
- enough to influence melting of DNA promoters
15
Q
what proteins are involved in DNA binding in bacteria?
A
- HU, IHF, H1, and protein P
16
Q
HU
A
dimer that condenses DNA into bead-like structure
17
Q
IHF
A
integration host factor
18
Q
H1
A
interacts with bent DNA
- not the same H1 in eukaryotes
19
Q
protein P
A
resembles protamine (found in sperm); very basic
20
Q
what is the eukaryotic genome comprised of?
A
- 50% DNA
- 10% RNA
- the rest is proteins, with half of the proteins histones
21
Q
how is the eukaryotic genome organized?
A
- loops of DNA about 60 kb but can range from 20-200
- composed of scaffold proteins
22
Q
MAR
A
- matrix attachment region
- DNA binds to nuclear matrix within nuclear membrane
- appear to be associated with scaffold proteins
- heterochromatin is strongly associated here
23
Q
euchromatin
A
- much less densely packed and dispersed
- only small portion transcribed
- more likely to be transcribed, does not mean it will be
24
Q
heterochromatin
A
- inactive
- two kinds: facultative and constitutive
25
constitutive heterochromatin
- regions that are not expressed, remain condensed
- structural and remain near centromeres
26
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
27
what are the 10, 30, and 50 nm fibers?
- 10 nm = beads on a string
- 30 nm = compact beads on a string
28
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
29
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
30
condensin 1
within primary loops to form subloops
31
condensin 2
- spirals that form the central structure of the condensed chromosome
32
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
33
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
34
what occurs in puff and balbiani rings?
intense RNA synthesis
- can tell the order based on short to long
35
what is a centriole?
- involved in the development of spindle fibers for cell division
- not found in all organisms
36
what is a centrosome?
- eukaryotic segregation device
- no DNA sequence but epigenetic modifications
37
what are MTOCs?
- microtubular organizing center
- found at centrioles at the poles and on each chromosome at the center
38
what is a kinetochore?
- 400 nm fiber found at centromere that is attached to the microtubules during mitosis
- provides MTOC for chromosome
39
what is the unusual yeast kinetochore?
Dam 1
40
budding yeast centromere structure
point centromere
41
insects, mammals, and plant centromere structure
regional centromeres
42
nematodes centromere structure
holocentric chromosome
43
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
44
why is the regional centromere more beneficial over the point centromere?
the point centromere can only accommodate a single turn of DNA
45
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
46
interphase nucleus
no condensed chromosomes
- chromosomes occupy specific territories within the nucleus and are not entangled
47
acentric fragment
does not get attached to mitotic spindle
