Chapter 10

Question 1

What is the difference between prokaryote (bacteria) and eukaryote genomes?

Answer 1

Bacteria have a singular circular chromosome, while eukaryotes have a complete set of linear, nuclear chromosomes.

Question 2

What are 4 things DNA sequences are necessary for?

Answer 2

Synthesis of RNA and cellular proteins, replication of chromosomes, proper segregation of chromosomes, compaction of chromosomes

Question 3

3 features of bacterial and eukaryotic chromosomes

Answer 3

general organization of functional sites on a chromosome, transposition (transposable elements can move to different sites within chromosomes), and mechanisms of chromosome compaction

Question 4

Intergenic regions of bacterial chromosome

Answer 4

Nontranscribed DNA between adjacent genes

Question 5

Where is the bacterial chromosome found in the cell?

Answer 5

The nucleoid- not bound by a membrane, DNA in direct contact with cytoplasm

Question 6

How does the bacterial chromosome fit into the cell? What shape does it take?

Answer 6

Formation of loop domains (microdomains, typically 10,000bp) helps compact DNA 1000-fold. Macrodomains pull microdomains together.

Question 7

What protein is used to form microdomains and macrodomains?

Answer 7

DNA-binding proteins called nucleoid-associated proteins (NAPs)

Question 8

What is a second way bacterial chromosomes become more compact?

Answer 8

DNA supercoiling (underwinding and over-winding of the DNA double helix)

Question 9

How is a negative supercoil formed (a topoisomer)?

Answer 9

A 360 degree left hand twist resulting in 12.5bp per turn (DNA too stretched out) or a supercoil formed that brings the number of bp back to 10 per turn

Question 10

How is a positive supercoil formed?

Answer 10

A 360 degree right hand twist that results in an 8.3 bp per turn helix (DNA to tight) or a supercoil formed that brings the number of bp back to 10 per turn

Question 11

What are two major effects of negative supercoiling in the bacterial chromosome?

Answer 11

Helps in the compaction of the chromosome (form new loop), and creates tension that may be released by DNA strand separation

Question 12

What two enzymes control supercoiling in bacteria?

Answer 12

DNA gyrase (topoisomerase II) - introduces negative supercoils and relax positive supercoils
DNA topoisomerase I - relaxes negative supercoils

Question 13

How can bacterial diseases be cured/alleviated?

Answer 13

By blocking the function of gyrase, which is crucial for bacteria’s survival (Quinolones and Coumarins inhibit gyrase)

Question 14

3 types of DNA sequences required for chromosomal replication and segregation

Answer 14

Origins of replication, centromeres, telomeres

Question 15

What is the difference in number of origins of replication in bacteria and eukaryotes?

Answer 15

Bacteria has only one origin of replication whereas eukaryotes have many origins of replication interspersed about every 100,000 bps

Question 16

3 types of repetitive sequences

Answer 16

Unique/non-repetitive, moderately repetitive, and highly repetitive

Question 17

What are unique/non-repetitive sequences?

Answer 17

Found once/a few times in genome, includes protein-encoding genes as well as intergenic regions

Question 18

What are moderately repetitive sequences?

Answer 18

Found a few hundred/several thousand times, genes for rRNA and histones, sequences that regulate gene expression and translation, transposable elements

Question 19

What are highly repetitive sequences?

Answer 19

Found tens of thousands/millions of times, each copy relatively short, sequences may be interspersed throughout genome or clustered together in tandem arrays

Question 20

What are transposable elements (TEs)?

Answer 20

“Jumping genes,” aids in transposition by integrating it’s small segments of DNA into new location in genome

Question 21

What are two transposition pathways that transposable elements move by?

Answer 21

Sample transposition - TE moves to a new target site
Retrotransposition - TE moves via an RNA intermediate (slide 28 has good pic)

Question 22

Direct repeats (DRs)

Answer 22

Identical base sequences oriented in same direction and repeated, flanking TEs

Question 23

Inverted repeats

Answer 23

DNA sequences that are identical/similar but run in opposite directions, flanking insertion element (simplest TE), may contain gene for enzyme transposase (catalyzes transposition event)

Question 24

Simple transposon

Answer 24

Carries one or more genes not required for transposition (pic on slide 30)

Question 25

LTR Retrotransposons

Answer 25

Related to retroviruses, contain long terminal repeats (LTRs) at both ends, encode virally related proteins like reverse transcriptase and integrase

Question 26

Non-LTR retrotransposons

Answer 26

Don’t resemble retroviruses in having LTR sequences, may contain gene that codes for protein that functions as reverse transcriptase and endonuclease

Question 27

Autonomous elements

Answer 27

“complete” transposable elements containing all information necessary for transposition or retrotransposition

Question 28

Nonautonomous element

Answer 28

Lacks a gene such as one that encodes transposase or reverse transcriptase (which is necessary for transposition)

Question 29

Transposase

Answer 29

Catalyzes removal of TE and its reinsertion at another location (does the moving), recognizes inverted repeats at ends of TE and brings them close together (pic on slide 37)

Question 30

How does simple transposition affect copy number?

Answer 30

Transposition occurs after replication fork has passed through TE, so one TE can transpose ahead of fork where it’s copied again, resulting in one chromosome having one TE but the other chromosome has two copies

Question 31

Target-site primed reverse transcription

Answer 31

Non-LTR retrotransposons move by target-site primed reverse transcription, retrotransposon transcribed into RNA with a 3’ polyA tail, binds to site nicked by endonuclease, reverse transcriptase uses target DNA of the primer and makes a DNA copy of RNA (pic on slide 42)

Question 32

Nucleosome

Answer 32

Repeating structural unit within eukaryotic chromatin, composed of double-stranded segment of DNA wrapped around octamer of histone proteins

Question 33

Histone proteins

Answer 33

Contain many positively-charged amino acids that hold on to negatively charged DNA well, have globular domain and flexible/charged amino terminus/”tail”

Question 34

5 types of histones

Answer 34

Core histones (two of each make up octamer) - H2A, H2B, H3, H4
Linker histone - H1, binds to DNA in linker region, helps organize adjacent nucleosomes and create compact structure called the 30nm fiber (zigzag structure)

Question 35

What is the third level of compaction?

Answer 35

30nm fiber folds into loop domains carried out by SMC proteins or CTCF dimers (pic on slide 63)

Question 36

What is the difference between heterochromatin and euchromatin during interphase?

Answer 36

Heterochromatin - transcriptionally inactive, tightly compacted regions of chromosomes, loop domains compacted even further
Euchromatin - transcriptionally active, less condensed regions, 30nm fiber forms loop domains

Question 37

2 types of heterochromatin

Answer 37

Constitutive - always herterochromatic, permanently inactive with regard to transcription, usually have highly repetitive sequences
Facultative - can interconvert between euchromatin and heterochromatin

Question 38

2 multiprotein complexes that help form and organize metaphase chromosomes

Answer 38

Condensin - critical role in chromosome condensation
Cohesin - critical role in sister chromatid alignment (holds them together until middle of prophase)
Both contain Structural Maintenance of Chromosomes (SMC) Proteins (use ATP to catalyze changes in chromosome structure)