Ch.10: Molecular structure of chromosomes and transposable elements

Question 1

Transposition

Answer 1

short segments of DNA, called transposable elements (TEs - Discovered by Barbra McClintock), can move to different sites within chromosome; involves the integration of small segments of DNA
into a new location in the genome

Question 2

Describe the structure of bacterial chromosomes

Answer 2

-Loop domains function to compact the bacterial chromosome
-Bacteria use DNA-binding proteins called nucleoid-associated proteins (NAPs) to form microdomains and macrodomain
- Microdomains are typically 10,000 bp
-macrodomains that are 800,000 to 1,000,000 bp

Question 3

What is supercoiling? What is underwinding and overwinding?

Answer 3

formation of
additional coils due to twisting forces;
Underwinding: DNA is given a turn that unwinds the helix
and causes fewer turns (negative supercoil)
Overwinding: DNA is given a turn that overwinds the helix
and causes more turns (positive supercoil)

Question 4

What 2 main topoisomerase enzymes control supercoiling in bacteria?

Answer 4

-DNA gyrase ( DNA topoisomerase II)
Introduces negative supercoiling, using energy from ATP, relaxes positive supercoils, untangle intertwined DNA molecules;
Two main classes of drugs inhibit topoisomerase II:
1. Quinolones
2. Coumarins

-DNA topoisomerase I
Relaxes negative supercoil

Question 5

What is the mechanism of action of DNA gyrase?

Answer 5

DNA gyrase binds to DNA, cuts it, ligates the cut DNA back together
in a process that uses two ATPs to introduce two negative supercoils

Question 6

What are the 3 types f DNA sequences that are required for chromosomal replication and segregation?

Answer 6

• Origins of replication: Each chromosome contains many origins of replication necessary to initiate DNA
  replication that are interspersed about every 100,000 base pairs
• Centromeres: forms a recognition site for the
  kinetochore proteins; required for chromosome sorting during mitosis and meiosis
• Telomeres: specialized regions at the ends of chromosomes important in replication and for stability

Question 7

Sequence complexity can be…?

Answer 7

unique or non-repetitive, moderately repetitive
or highly repetitive

Question 8

Unique/non-repetitive sequences

Answer 8

s protein-encoding genes as well as intergenic regions

Question 9

Moderately repetitive sequences

Answer 9

Includes genes for rRNA and histones, sequences that regulate gene expression and translation and
transposable elements

Question 10

Highly repetitive sequences

Answer 10

• Alu family of transposable elements in humans that are approximately 300 bp long
  -Other highly repetitive sequences are clustered together in tandem arrays

Question 11

General characteristics and different types of transposons

Answer 11

• All transposons have a terminal direct repeat (DR), which is also called a target-site duplication
• Insertion elements are characterized by the presence of a terminal inverted repeat
• Long terminal repeat (LTR) retrotransposons and non-LTR retrotransposons are characterized by the presence of a reverse transcriptase gene

Question 12

Autonomous vs. non-autonomous transposons

Answer 12

• autonomous elements (complete) contain all of the
  information necessary for transposition or retrotransposition
• Nonautonomous element lacks a gene such as one that
  encodes transposase or reverse transcriptase

Question 13

Transposons can…

Answer 13

carry extra genes, such as genes that encode antibiotic resistance (horizontal transfer)

Question 14

LTR retrotransposons vs. non-LTR retrotransposons

Answer 14

Both carry a reverse transcriptase that copies the sequence for insertion
somewhere else in the chromosome but
LTR retrotransposons contain a long terminal repeat (LTR) sequence

Question 15

Insertion elements and transposons vs. retrotransposons

Answer 15

-Insertion elements and transposons excise themselves and move to a new location on the chromosome
-Retrotransposons make a copy of themselves and insert the copy into a new location on the chromosome

Question 16

Some repetitive sequences due to the proliferation of transposons

Answer 16

-LINEs (long interspersed elements): Occur at 20,000 to 1,000,000 copies per genome (17% of the human genome)
-SINEs (short interspersed elements): Less than 500 bp in length; The SINE Alu sequence is present at about 1,000,000 copies in human genome (10% of the genome)

Question 17

Describe the structure of eukaryotic chromosomes in nondividing cells

Answer 17

compact DNA-protein complex is called chromatin; nucleosome: repeating structural unit within eukaryotic chromatin that is
composed of a double-stranded segment of DNA wrapped around an octamer of histone proteins; A histone octamer is composed of two copies each of four different histone proteins (H1-4, H1 links nucleosomes together and compacts them

Question 18

Korenberg and Null

Answer 18

The beads-on-a-string model of nucleosome structure by Kornberg and Marcus Null tested Kornberg’s model where DNase I should preferentially cut DNA in the linker region

Question 19

Who demonstrated the importance of H1 histone in organizing the nucleosome and how?

Answer 19

Fritz Thoma- Used chromatography and high salt to remove the H1 histones (less compaction)

Question 19

What do nucleosomes form?

Answer 19

a compact structure termed the 30 nm fiber

Question 20

What are the 2 types of heterochromatin?

Answer 20

-Constitutive heterochromatin: Regions that are always heterochromatic
Permanently inactive with regard to transcription

-Facultative heterochromatin:
Regions that can interconvert between
euchromatin and heterochromatin

Question 20

Euchromatin

Answer 20

Less condensed regions of chromosomes; Transcriptionally active

Question 21

Heterochromatin

Answer 21

Tightly compacted regions of chromosomes; Transcriptionally inactive (in general

Question 22

How do Condensin and cohesin promote the compaction of metaphase chromosomes?

Answer 22

• Condensin: Plays a critical role in chromosome condensation
• Cohesin: Plays a critical role in sister chromatid alignment
  -during Interphase, den II enters the nucleus while hes I is in the cytoplasm