6. the nucleus: DNA packaging Flashcards Preview

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Flashcards in 6. the nucleus: DNA packaging Deck (44)
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1

the human genome

-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

2

Chromatin structure is only visible as ______ and ______ regions

denser, lighter

3

dark heterochromatin is located around the ______

nucleus periphery

4

active genes, in the euchromatin are located toward the _______

interior nucleus

5

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

transcriptional

6

DNA organization level 1: histones

-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

7

nucleosomes

-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

8

Histone H1 (fifth type)

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

9

DNA organization Level 2: 30 nm fibres

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

10

DNA organization level 3: looped domains

-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

11

MARs

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

12

Scaffold proteins includes the following:

-nuclear matrix
-topoisomerase II
-insulator protein
-nuclear lamina

13

nuclear matrix

-a protein fibre framework
-major organizing structure for RNA polymerase (makes messenger RNA), RNA processing, DNA replication

14

Topoisomerase II

-an untangling protein (for unwinding DNA)

15

insulator protein

keeps loops separate

16

nuclear lamina

lamins bind telomeres and alpha satellite DNA of the centromere

17

Nuclear scaffold can be observed by

digesting away all DNA and removing all histones

18

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

-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

Alpha satellite DNA is comprised of _____ nucleotide repeats

171

20

histone code

-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

Modified types of histones

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

22

H2A.X

DNA being repaired

23

H2A.Z

DNA transcribed by RNA polymerase II

24

CNEP-A

version of H3
on the centromere, kinetochore assembly

25

macroH2A

Barr body
keeps chromatin condensed and inactive

26

What does the phosphorylating?

ATM

27

Acetylated histones

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

28

Phosphorylated histones

can increase or decrease DNA winding on histones

29

methylated histones

-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

euchromatin

open, dispersed, potentially active