Lecture 11 - Structure of Eukaryotic Genomes (Nuclear): Simon Whitehall

Question 1

What is the C-Value paradox?

Answer 1

Gene number does not increase linearly with genome size.

Question 2

What are the 4 features of Human eukaryotic genomes in terms of compactness?

Answer 2

• Relatively low gene density.
• Relatively high Introns per gene.
• Relatively high Amount of genome occupied by genome wide repeats.
• Protein coding genes account for 2% of human genome.

Question 3

What are the 3 basic properties of prokaryotic chromosomes?

Answer 3

• Single Circular chromosome.
• Single Origin of Replication terminating at a single site terAB.
• Replicates bi-directionally with 2 replication forks (sites of DNA synthesis).

Question 4

What are the 3 basic properties of eukaryotic chromosomes?

Answer 4

• Split into a set of linear chromosomes.
• All eukaryotes have at least 2 chromosomes (no known exceptions)
• Have multiple origins of replication.

Question 5

How do banding patterns arise in Human Karyograms?

Answer 5

By the use of dyes/staining - e.g using GIEMSA. The dyes have preferences for certain base pairs depending upon the treatment.

Question 6

Explain G-Banding

Answer 6

Procedure: Mild proteolysis followed by Giemsa

Banding Pattern:
Dark Bands are AT rich

Question 7

Explain R-Banding

Answer 7

Procedure: Heat denaturation followed by Giemsa

Banding Pattern: Dark bands are GC rich.

Question 8

Explain Q-Banding

Answer 8

Procedure: Stain with Quinacrine

Banding Pattern: Dark bands are AT rich.

Question 9

Explain C-Banding

Answer 9

Procedure: Barium hydroxide followed by Giemsa

Banding Pattern: Dark bands are constitutive heterochromatin

Question 10

Which 2 banding types produce the same banding pattern?

Answer 10

G-Banding and Q-Banding.

Question 11

When would you find condensed and decondensed chromosomes?

Answer 11

Condensed: Mitosis
Decondensed: Interphase

Question 12

What is a chromatid, and when is it visible in the nucleus?

Answer 12

Chromatid is a condensed chromosome seen during mitosis, when not in mitosis they occupy a distinct territory within the nucleus.

Question 13

What is the function of the Centromere?

Answer 13

Region where sister chromatids are held together.

In higher eukaryotes, they act as the assembly site for a protein complex called Kinetochore which plays a key role in Chromosome Division.

Question 14

As the centromere moves further up the chromosome,, the chromosome’s X shape is skewed. What are the 4 different names for these categories of chromosome?

Answer 14

Perfect X: Metacentric

Short upper arm: Submetacentric

Very short upper arm: Arcocentric

Practically non-existent upper arm: Telocentric.

Question 15

What are the short and long arms of chromosomes referred to as?

Answer 15

p(etite) = short arms
q = long arms

Question 16

What are teleomeres, and what are their major functions?

Answer 16

Telomeres occupy the very tip of each of the sister chromatids. They are composed of hundreds of copies of repeated motif
5’ TTAGGG 3’

They recognize real or abnormal chromosome ends caused by a chromosome break. This is important to stop joining fellow telomeres together.

Question 17

What is the “End-Replication Problem?”

Answer 17

During DNA replication, 3’ Terminal end cannot be copied, so it appears as a ssDNA overhang. Over successive replication cycles, the overhang gets degraded and leads to progressive chromosome shortening -> eventually leading to a telomere crisis where important parts of the strand are being degraded.

Question 18

What is “replicative senescence” ?

Answer 18

A limitation in the number of times that cells can divide; appears to be a basic feature of most cells.

Question 19

What is the role of Telomerase in solving the “End-Replication Problem?”

Answer 19

It prevents chromosome shortening by adding ‘TTAGG’ repeats to the overhang, which allows replication of this area - thereby extending the chromosome.

Question 20

What are the 3 main properties of Telomerase?

Answer 20

We are born with full length telomeres due to activity of telomerase in development.

In almost all somatic cells, telomerase is turned off.

Telomeres shorten during our life times during each cell division, eventually leading to defective chromosomes -> cell death. This mechanism is called replicative cell senescence, and protects against cancer.

Question 21

What is a key experiment involving Telomerase?

Answer 21

Fibroblasts (skin cells) go through 60 divisions in culture. If telomerase function is provided, they replicate indefinitely.

Question 22

How is DNA packaged (in eukaryotes)?

Answer 22

Genomic DNA in eukaryotes associated with histones. DNA wraps around twice around an octamer of histones -> Nuclesome. Nucleosome is the basic repating unit of chromatin -> forms array leading to chromatin fibre. Fibres then proceed to get thicker and thicker.

Question 23

What is the difference between Euchromatin and Heterochromatin?

Answer 23

Euchromatin: Relatively uncondensed chromatin associated with expressed genes.

Heterochromatin: Condensed chromatin associated with repetitive gene poor regions that are inactive.

Question 24

What are minichromsomes?

Answer 24

Relatively short chromosome that are rich in genes.

Question 25

What are B Chromosomes?

Answer 25

Additional chromosome possed by some but not all individuals in a population (common in plants, but also seen elsewhere)

Question 26

What are Holocentric chromosomes?

Answer 26

Instead of a single centromere, they have multiple kinetochores throughout their length.

Question 27

What are Polytene Chromosomes?

Answer 27

Giant chromosomes - seen in larvae of drosophilia - historically important for genetics.