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Cell Biology > 6. the nucleus: DNA packaging > Flashcards

6. the nucleus: DNA packaging Flashcards

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1
Q

the human genome

A
  • is written in 6*10^9 nucleotide bases
  • contains the ~22,00 different genes
  • is divided into 46 chromosomes, each an unbroken strand
  • is a total of 2m long in the nucleus of 10um in diameter
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2
Q

Chromatin structure is only visible as ______ and ______ regions

A

denser, lighter

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3
Q

dark heterochromatin is located around the ______

A

nucleus periphery

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4
Q

active genes, in the euchromatin are located toward the _______

A

interior nucleus

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5
Q

While chromosomes haves have their own territories, there can be some overlap, so they they can share some of the ____________ machinery.

A

transcriptional

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6
Q

DNA organization level 1: histones

A
  • DNA winds around the nucleosomes, which are composed of a group of positively charges, highly conserved proteins- histones
  • DNA is held by the histones due to non-covalent bonds, especially ionic bonds between negatively charged phosphate backbone of DNA and positive charge of histone
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7
Q

nucleosomes

A
  • made up of four types of histones
  • two of each: H2A, H2B, H3, H4
    * DNA wraps around the nucleosomes 1.8 turns or 146 nucleotide bases per nucleosome
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8
Q

Histone H1 (fifth type)

A

linker histone

  • links adjacent nucleosome core particles
  • a total of 168 nucleotide bases per unit
  • 7.1 packing ratio, the fibre is 10nm thick
  • 6-7 fold shortening
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9
Q

DNA organization Level 2: 30 nm fibres

A

spontaneous assembly of adjacent nucleosomes results in a 40:1 condensation in length, with 30 nm thick fibres

  • H1 may bind adjacent nucleosomes
  • N-terminal tails of H4 may extend far enough to reach other nucleosome histones
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10
Q

DNA organization level 3: looped domains

A
  • the 30 nm fibres gather into supercoiled loops
  • loops are tethered to protein nuclear scaffold
  • cohesin- ring shaped protein may maintain the loops
  • DNA strands associate with nuclear matrix
    • form loops of 20,000 to 100,000 bases
    • AT-rich domains on DNA form MARs (matrix associated region)
    • includes alpha satellite and other non-coding DNA
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11
Q

MARs

A

DNA sequence that has affinity for nuclear matrix; note that DNA loop can be moved to facilitate transcription

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12
Q

Scaffold proteins includes the following:

A
  • nuclear matrix
  • topoisomerase II
  • insulator protein
  • nuclear lamina
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13
Q

nuclear matrix

A
  • a protein fibre framework

- major organizing structure for RNA polymerase (makes messenger RNA), RNA processing, DNA replication

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14
Q

Topoisomerase II

A

-an untangling protein (for unwinding DNA)

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15
Q

insulator protein

A

keeps loops separate

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16
Q

nuclear lamina

A

lamins bind telomeres and alpha satellite DNA of the centromere

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17
Q

Nuclear scaffold can be observed by

A

digesting away all DNA and removing all histones

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18
Q

DNA organizing Level 4: mitotic chromosomes (a 10,000-fold decrease in length)

A
  • also have looped domain structure
    • no nucleus when chromosomes in this state
    • DNA loops on Condensin protein
    • more compact than interphase chromatin
    • phosphorylation by MPF
  • centromere is a site of extreme condensation
    • contains alpha-satellite DNA
    • binds to proteins, including the kinetochore
19
Q

Alpha satellite DNA is comprised of _____ nucleotide repeats

A

171

20
Q

histone code

A
  • DNA is frequently being transcribed and duplicated
  • Necessary machinery has to work around nucleosomes
    • the cell makes DNA more or less accessible to other proteins by modifying histones
  • mechanisms of Histone modification
    • replacement with modified types of histone
    • chemical modification of the histones
21
Q

Modified types of histones

A
  • H2A.X
  • H2A.Z and H33.3
  • CNEP-A (version of H3)
  • macroH2A
22
Q

H2A.X

A

DNA being repaired

23
Q

H2A.Z

A

DNA transcribed by RNA polymerase II

24
Q

CNEP-A

A

version of H3

on the centromere, kinetochore assembly

25
Q

macroH2A

A

Barr body

keeps chromatin condensed and inactive

26
Q

What does the phosphorylating?

A

ATM

27
Q

Acetylated histones

A

looser DNA binding
HDAC- histone deacetylse (removes acetyl group)
HAT- histone acetyl transferase

28
Q

Phosphorylated histones

A

can increase or decrease DNA winding on histones

29
Q

methylated histones

A
  • alter the accessibility of DNA to processing enzymes
  • alter binding to organizational structures such as nuclear matrix
  • often tighter DNA binding
  • eg methylation of H3 leads to HP1 binding, which helps form heterochromatin
30
Q

euchromatin

A

open, dispersed, potentially active

31
Q

heterochromatin

A

during interphase about 10% of the chromatin remains in a compact state similar to the mitotic chromosome; this DNA is not transcribed or translated

32
Q

Constitutive heterochromatin

A

condensed at all times
includes:
1) AT-rich satellite DNA at the centromere;
2) the telomeres (ends of the chromosomes)

33
Q

facultative heterochromatin

A

transient condensation, contains temporarily inactive genes

34
Q

In humans, gender is determined by the sex chromosomes:

A

females: two x chromosomes
males: one x and one y chromosome

35
Q

x and y chromosomes look very different:

A

almost all the gens on the x have no counterpart on the y

36
Q

To ensure that males and females have equal levels of gene expression derived from the x chromosome what happens?

A

one x in every female cell is inactivated

which x is apparently random

37
Q

inactivation of an x chromosome requires a gene on that chromosomes called ______

A

XIST

38
Q

XIST

A

encodes a large molecule of RNA

39
Q

XIST RNA

A
  • accumulates along the x chromosome containing the active XIST gene and proceeds to inactivate almost all of the other genes on that chromosome
  • does not travel over to the other x chromosome in the nucleus
40
Q

Barr bodies

A

are inactive x chromosomes painted with XIST RNA

41
Q

inactive x chromosome is

A

neatly straight and organized

42
Q

How is the Barr body condensed?

A
  • XIST RNA induces several later events (by recruiting various enzymes):
    • deacetylation of H3
    • methylation of H3
    • Ubiquitination of H2A
  • H2A is replaced with macroH2A
  • all these changes are undone in egg cells
43
Q

what does random inactivation of x result in?

A

mosaic patterns of gene expression
ex. calico cats: always female ( except in rare XXY males )
*x chromosome has gene for coat colour
*the gene can encode either a black pigment of orange
*since males have only one x, they can be either black or orange, not both
-the X chromosome inactivation in females is random, so different patches of epidermal cells can have different colour genes
(the gene for white coat is on another chromosome)

44
Q

interphase chromatin

A
  • storing DNA is an exercise in organization
  • although not easily seen in interphase, each unwound chromosome has a defined territory within the nucleus
    * held in place on the nuclear matrix and nuclear laimina, ie. protein frameworks
    * where each chromosome is positioned can affect the expression of its genes

Cell Biology (16 decks)

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