Sept 27

Question 1

Does interphase have 10 and or 30nm DNA?

Answer 1

It has both

Question 2

How are 10 and 30 nm chromatin structured?

Answer 2

10 nm is beads on a string, chromatin is wrapped 1.5 ish times around histone core, then have short DNA linker region before the next nucleosome. 30 nm is 10 nm but has H1 interacting with DNA the histone

Question 3

When does maximum condensation of the chromosomes occur?

Answer 3

During M phase

Question 4

What get after incomplete and complete digestion of 10 nm DNA?

Answer 4

At complete digestion get 1 band, representing DNA around histones, everything else broken down. In incomplete digestion get bands 200 bp apart, so know nuclosome and linker DNA are about 200 bp each

Question 5

What 2 AA’s are very rich in histones?

Answer 5

Lys and Arg

Question 6

Why did histone proteins treated with SDS page not travel as far in the gel as expected?

Answer 6

They are positively charged, so even with SDS they still were less neg than other proteins, and it looked like they were bigger proteins than acutallity as they traveled slower towards the positive electrode

Question 7

What secondary structures make up histone subunits?

Answer 7

Have a-helices and a N terminal tail

Question 8

What is the structure of each histone subunit?

Answer 8

H3 and H4 bind to form a tetramer (2 of each), then H2A and H2B form a heterodimer (still 2 of each), so 8 proteins total in histone core

Question 9

How does H2A +H2B dimer bind to H3and 4 tetramer?

Answer 9

A H2A and B dimer binds to each side of the H3/4 tetramer, forms a sandwich

Question 10

What histone subunits bind to DNA?

Answer 10

The H3 and H4 tetramer

Question 11

Where on DNA does the H3 and H4 tetramer?

Answer 11

They hydrogen bond to the minor grooves of DNA, the grooves are not as deep

Question 12

Why do histones have lys and arg ?

Answer 12

To bind to the neg PO4 backbone of DNA

Question 13

Are histone tials needed for DNA to bind? Do they stabilize it though?

Answer 13

Not needed to bind, but are Pos so interact with neighbouring nuclosomes to stabilize, charge neutralization so facilitate compaction

Question 14

What AA do histone tails have a lot of, what function?

Answer 14

Cys, they can be modified a lot

Question 15

Do tails guide DNA wrapping in L-handed way to induce neg supercoiling?

Answer 15

Yes

Question 16

What enzymes keep DNA relaxed in eukaryotes and which ones introduce supercoiling + and - in prokaryotes?

Answer 16

Eukaryotes have topoisomerases to keep DNA relaxed. Prokaryotes have gyrase to introduce neg supercoilding, and reverse gyrase to introduce pos supercoiling

Question 17

Where as a whole (end, middle) does H3 and H4 tetramer bind to DNA, does it help H2A and H2B dimers bind?

Answer 17

Yes the tetramer binds to middle and ends of the DNA (bends DNA around it), and helps the H2A and H2B dimers bind to DNA as well

Question 18

Are histone to DNA H bonds sequence dependent?

Answer 18

No

Question 19

Heterochromatin vs euchromatn for level of staining?

Answer 19

Euchromatin is less dense so less staining than heterochromatin

Question 20

Where are eu and heterochromatin organized within the nucleus

Answer 20

Euchromatin is in the center of the nucleus, heterochromatin is close to the nuclear scaffold which is close to the nuclear envelope

Question 21

solenoid vs zigzag nucleosomes structures?

Answer 21

Solenoid is a 6 pointed star with a hollow center, has linker DNA between each nuclosomes, zig zag does not have hollow center, has linker DNA there.

Question 22

Does zigzag or solenoid work better for nuclosomes with shorter linker DNA?

Answer 22

Solenoid works better

Question 23

Can DNA be accessed by DNA-dependent enzymes (polymerases etc) once in 30 nm structure?

Answer 23

Not really