1.) Genes and Chromosomes I

Question 0

Largely, what are the three categories of the eukaryotic genome?

Answer 0

Transposons (45%), Genes (30%), and miscellaneous (25%).

Question 1

What is the best definition for a gene?

Answer 1

All of the DNA that is required to encode the primary sequence of some final gene product (ie the final product could be RNA or a protein).

Question 2

How much of the human genome becomes encoded into an expressible gene?

Answer 2

30% of the genome is converted into genes, but only 1.5% of the entire genome will become mature RNA (aka expressed into functional genes). The other 28.5% are introns or non-coding segments.

Question 3

Approximate number of genes?

Answer 3

25000

Question 4

What is the name for the sequences that are typically seen at the ends of DNA?

Answer 4

Telomeres

Question 5

How can you induce supercoiling?

Answer 5

If you hold one end of a double helical strand constant, then at the other end pull apart the strands. This is how topoisomerases function.

Question 6

What is topology?

Answer 6

The study of the properties of an object that do not change under continuous deformations.

Question 7

A change in the state of DNA from its relaxed state to its strained state is a result of…

Answer 7

Underwinding or overwinding the DNA (e.g. 8 turns to 7 turns is underwinding). This is aided via topoisomerases.

Question 8

Topoisomerases will change the _________ of DNA strands.

Answer 8

Linking number.

Question 9

What is the difference between topoisomerase I and topoisomerase II?

Answer 9

Topoisomerase I will change the linking number by increments of 1, and only breaks one strand.
Topoisomerase II will change it by increments of two by breaking two strands of DNA simultaneously (see slide 39).

Question 10

Which is more compact, underwinding or overwinding DNA?

Answer 10

Both will compact the DNA from its relaxed state. (needs verification). Check out Slide 38.

Question 11

In slide 38, each band on the gel represents a change in…

Answer 11

the linking number, by one.

Question 12

Why is supercoiling DNA important?

Answer 12

It is how we package DNA.

Question 13

Describe the higher order structures of compact DNA.

Answer 13

1. ) Loose/Free DNA. Double helix.
2. ) Nucleosome - wrapping of DNA around a histone. It is a colloidal structure of DNA around a nucleosome. “Beads on a string”
3. ) Chromatin - tightly packed nucleosomes. 30nm fiber.
4. ) One Loop - ~75000 base pairs
5. ) One rosette (6 loops)
6. ) One coil (30 rosettes)
7. ) Two chromatids/Chromosome - compact form of chromatin.

Question 14

The packaging of DNA around a histone gives about _____ fold compaction

Answer 14

7

Question 15

DNA histone wrapping yields a ______ handed ________ supercoil.

Answer 15

Left, solenoidal (negative).

Question 16

The tightly packing of histones, can be thought of as chromatin, or as a _________.

Answer 16

30nm fiber.