Genome Structure

Question 1

What is “C-value”?

Answer 1

The amount of DNA in the unreplicated haploid genome of an organism

Question 2

What are the units for measuring C-value?

Answer 2

Length in bp or meters

Mass in grams

Question 3

What is the C-value Paradox?

Answer 3

The inability to account for the DNA content of genomes based on complexity

Question 4

What are the 2 problems included in the C-value paradox?

Answer 4

1. ) C-value is higher than necessary

2. ) Large variations in C-value for closely related organisms whose apparent complexity varies little

Question 5

What are 2 factors that help to resolve the C-value paradox?

Answer 5

1. ) Junk DNA

2. ) Repetitive DNA

Question 6

Why is renaturation concentration dependent while denaturation is not?

Answer 6

Single-stranded molecules must find each other in solution, so when DNA is at a higher concentration, it is easier to find other molecules and reanneal

Question 7

Why must DNA be reduced to smaller fragments for renaturation?

Answer 7

If the fragments are too large, they will get tangled and won’t be able to renature

Question 8

What are 3 methods used to denature DNA?

Answer 8

1. ) Heat
2. ) Alkali
3. ) Acid

Question 9

Why is slow cooling important for renaturation?

Answer 9

If quickly cooled, the DNA will collapse into a compact random coil in which some bases are hydrogen bonded. Slow cooling allows for better hybridization between single strands

Question 10

What is nucleation?

Answer 10

An event in which regions of complementary bases on opposite strands find each other and begin to base pair and form a double helix

Question 11

When does “zipping up” occur?

Answer 11

When nucleation is correct and if there are complementary bp’s

Question 12

What are 2 reasons that renaturation will never be complete?

Answer 12

1. ) Random shearing leaves some regions unpaired
2. ) As renaturation progresses, the concentration of single-stranded molecules decreases and the rate of renaturation drops

Question 13

What is the importance of stringency?

Answer 13

When correct, it prevents tangles of random coils that could form in even relatively short segments of DNA

Question 14

What happens when the stringency is too low?

Answer 14

Non-specific hybridization can occur

Question 15

What are Cot Curves?

Answer 15

Curves that examine the renaturation of DNA and the kinetics of renaturation

Question 16

What is the relationship between the rate of renaturation and the length (or complexity) of the re-associating DNA?

Answer 16

Inversely proportional; more complex genomes renature more slowly

Question 17

Define Complexity

Answer 17

The length of the unique-sequence DNA; repeated sequences add to the complexity only once no matter how often they are repeated

Question 18

What does Cot1/2 represent?

Answer 18

A specific Cot at which half the renaturing molecules are single-stranded and half are double-stranded; should be the same for any concentration of DNA that you test

Question 19

Why plot Cot?

Answer 19

Experiments using a single concentration of DNA would take years

Question 20

What is the rate-limiting step in renaturation?

Answer 20

The formation of productive nucleations