6. the nucleus: DNA packaging

Question 1

the human genome

Answer 1

• 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

Question 2

Chromatin structure is only visible as ______ and ______ regions

Answer 2

denser, lighter

Question 3

dark heterochromatin is located around the ______

Answer 3

nucleus periphery

Question 4

active genes, in the euchromatin are located toward the _______

Answer 4

interior nucleus

Question 5

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

Answer 5

transcriptional

Question 6

DNA organization level 1: histones

Answer 6

• 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

Question 7

nucleosomes

Answer 7

• 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

Question 8

Histone H1 (fifth type)

Answer 8

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

Question 9

DNA organization Level 2: 30 nm fibres

Answer 9

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

Question 10

DNA organization level 3: looped domains

Answer 10

• 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

Question 11

MARs

Answer 11

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

Question 12

Scaffold proteins includes the following:

Answer 12

• nuclear matrix
• topoisomerase II
• insulator protein
• nuclear lamina

Question 13

nuclear matrix

Answer 13

• a protein fibre framework

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

Question 14

Topoisomerase II

Answer 14

-an untangling protein (for unwinding DNA)

Question 15

insulator protein

Answer 15

keeps loops separate

Question 16

nuclear lamina

Answer 16

lamins bind telomeres and alpha satellite DNA of the centromere

Question 17

Nuclear scaffold can be observed by

Answer 17

digesting away all DNA and removing all histones

Question 18

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

Answer 18

• 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

Question 19

Alpha satellite DNA is comprised of _____ nucleotide repeats

Answer 19

171

Question 20

histone code

Answer 20

• 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

Question 21

Modified types of histones

Answer 21

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

Question 22

H2A.X

Answer 22

DNA being repaired

Question 23

H2A.Z

Answer 23

DNA transcribed by RNA polymerase II

Question 24

CNEP-A

Answer 24

version of H3

on the centromere, kinetochore assembly

Question 25

macroH2A

Answer 25

Barr body | keeps chromatin condensed and inactive

Question 26

What does the phosphorylating?

Answer 26

ATM

Question 27

Acetylated histones

Answer 27

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

Question 28

Phosphorylated histones

Answer 28

can increase or decrease DNA winding on histones

Question 29

methylated histones

Answer 29

- 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

Question 30

euchromatin

Answer 30

open, dispersed, potentially active

Question 31

heterochromatin

Answer 31

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

Question 32

Constitutive heterochromatin

Answer 32

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

Question 33

facultative heterochromatin

Answer 33

transient condensation, contains temporarily inactive genes

Question 34

In humans, gender is determined by the sex chromosomes:

Answer 34

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

Question 35

x and y chromosomes look very different:

Answer 35

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

Question 36

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

Answer 36

one x in every female cell is inactivated | which x is apparently random

Question 37

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

Answer 37

XIST

Question 38

XIST

Answer 38

encodes a large molecule of RNA

Question 39

XIST RNA

Answer 39

- 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

Question 40

Barr bodies

Answer 40

are inactive x chromosomes painted with XIST RNA

Question 41

inactive x chromosome is

Answer 41

neatly straight and organized

Question 42

How is the Barr body condensed?

Answer 42

- 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

Question 43

what does random inactivation of x result in?

Answer 43

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)

Question 44

interphase chromatin

Answer 44

- 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