DNA Structure and Packaging

Question 1

What are the 4 bases in DNA? Which ones are purines and which ones are pyrimidines?

Answer 1

Adenine and guanine - purines

Cytosine and thymine - pyrimidines

Question 2

What type of bond links nucleotides together?

Answer 2

Phosphodiester bonds

Question 3

What creates the 5’ to 3’ polarity of nucleic acid strands?

Answer 3

The position of the phosphodiester bonds. One end has a free 5’ phosphate and the other has a free 3’ OH

Question 4

What is a genome?

Answer 4

The complete set of genetic information in a single cell in an organism

Question 5

What is a chromosome?

Answer 5

A molecule made of nucleic acids that contains the genetic information of an organism

Question 6

What is a gene?

Answer 6

A segment on a chromosome that encodes a functional product

Question 7

What two methods do prokaryotes use to package DNA?

Answer 7

Looping and supercoiling

Question 8

How do DNA binding proteins help with looping DNA in prokaryotes?

Answer 8

They bend the DNA and make it form a floret structure that has stable loops

Question 9

What is supercoiling?

Answer 9

When the DNA double helix is coiled up and twisted onto itself

Question 10

How is supercoiling induced in prokaryotic cells?

Answer 10

The linear DNA is unwound by one turn then sealed into circular DNA. This creates a strained circle at 11.67 base pairs per turn, and the DNA undergoes supercoiling to revert back to the stable 10.5 base pairs

Question 11

What is the general mechanism of how topoisomerases work?

Answer 11

They make a nick in the strand, untwist the DNA by one turn, then seal the strands back together

Question 12

What types 1 and 2 topoisomerases do?

Answer 12

Type 1 makes a temporary single strand nick, type 2 makes a temporary double strand break

Question 13

What kinds of topoisomerases do prokaryotes have? Eukaryotes?

Answer 13

Prokaryotes have topoisomerases that induce supercoiling and others that remove it. Eukaryotes only have topoisomerases to remove supercoiling

Question 14

How is supercoiling maintained?

Answer 14

DNA binding proteins

Question 15

What is the smallest level of DNA packaging in eukaryotes?

Answer 15

The nucleosomes

Question 16

What is chromatin?

Answer 16

A complex of DNA and all packaging proteins

Question 17

What was the experiment that determined how much DNA was bound to proteins vs not bound to proteins in a nucleosome?

Answer 17

They added micrococcal nuclease that cleaves any unbound DNA, and saw only one band on the gel for 147 bp. That indicated how much DNA was bound to a protein. They then added less micrococcal nuclease to get incomplete cleavage, and the nuclease on average cut at the halfway point between proteins to determine that there are 50 base pairs in between each nucleosome

Question 18

How much DNA is wrapped around the protein in a nucleosome and how much DNA is in between nucleosomes?

Answer 18

147 base pairs are wrapped around the protein, 50 base pairs in between as linker DNA

Question 19

What is the structure of the histone in a nucleosome?

Answer 19

An octamer, made of 8 subunits of 4 types with 2 of each

Question 20

What are the 4 types of subunits in the histone octamer?

Answer 20

H3, H4, H2A and H2B

Question 21

What is the charge on the histone proteins?

Answer 21

Positive, it binds to the negatively charged DNA

Question 22

What is the purpose of the histone protein tails?

Answer 22

They are flexible and about 19-39 amino acids long. They are believed to interact with neighbours and help form the 30 nm fibre and higher levels of packaging

Question 23

What are the two types of linker histones? What do they do?

Answer 23

H1 and H5. They stabilize DNA entering and leaving the nucleosome

Question 24

What is the next level of packaging after the nucleosome?

Answer 24

The 30 nm fibre. The beads on a string structure of the nucleosomes get condensed into a fibre that is 30 nm wide

Question 25

What is the next level of packaging after the 30nm fibre?

Answer 25

30nm fibre is packaged into loops with scaffold proteins

Question 26

What is the highest level of packaging in eukaryotes?

Answer 26

Chromosomes

Question 27

What is euchromatin?

Answer 27

Packaged DNA that is relatively loose, which makes it easier for transcription to occur

Question 28

What is heterochromatin?

Answer 28

Packaged DNA that is much tighter. It squishes the nucleosomes together and stops transcription from occurring

Question 29

What is constitutive heterochromatin? Where is this seen?

Answer 29

DNA that is always in the tightly packed state. Found in structural components of the chromosome that don’t contain genes, so they don’t need to be unwound anyways, aka telomeres and centromeres

Question 30

What is facultative heterochromatin?

Answer 30

DNA that is sometimes euchromatin and sometimes heterochromatin, this only happens in a few situations

Question 31

What are protamines?

Answer 31

An alternative method of DNA packaging. They are positively charged proteins that bind to the major groove of DNA

Question 32

How do protamines allow DNA to be packaged more tightly than in nucleosomes?

Answer 32

They neutralize the negative charge on DNA, so it stops repelling itself

Question 33

What structure does DNA packaged with protamines form?

Answer 33

Toroid structures. They are planar and donut shaped so they can be stacked very closely together

Question 34

What type of cell is DNA packaged with protamines found in?

Answer 34

Mammalian sperm

Question 35

If protamines can pack DNA tighter than nucleosomes, why isn’t it used everywhere?

Answer 35

It ends up packed up even tighter than heterochromatin, so it is impossible for transcription to occur. This is not a problem for sperm, but will be for anything else