Organisation of Genomes

Question 1

What is a genome?

Answer 1

The genetic material of an organism or virus

Question 2

What exists in each “chromosome” for dividing and non-dividing cells?

Answer 2

One DNA double helix, which exists as decondensed chromatin

Question 3

Compare euchromatin and heterochromatin

Answer 3

Euchromatin is decondensed and thus transcriptionally active, but heterochromatin does not fully decondensed and is thus transcriptionally active.

Question 4

What happens to the DNA after S phase for dividing cells?

Answer 4

Each chromosome comprises two DNA double helices, which exists as

1. Decondensed chromatin (after S phase and before prophase)
2. Two identical sister chromatids (during nuclear division)

Question 5

Function of Centromere

Answer 5

Responsible for attaching chromosomes to the kinetochore microtubules during cell division

Question 6

How many pairs of chromosomes does a human genome have?

Answer 6

23 pairs

Question 7

How many sister chromatids does each chromosome have?

Answer 7

Two sister chromatids

Question 8

How many levels of condensation are there for packing of DNA in eukaryotics chromosomes?

Answer 8

3 levels

Question 9

What happens to the DNA during the FIRST level of condensation?

Answer 9

1. DNA is packed into nucleosomes to produce the nucleosome fibre (10-nm interphase chromatin fibre)
   - dsDNA coils 1 3/4 turns around the histone core, forming a nucleosome core.
   - Chromatin fibre = Nuclesomes + Linker DNA
2. The nucleosome consisting the DNA wound twice around a protein core composed of an octamer of 4 histone molecules, two of each histones.
3. Histones leave the DNA only briefly during DNA replication and gene expression.
   - Histones are small proteins with a high concentration of basic residues (postively-charged R groups), which interact with the negatively-charged sugar-phosphate backbone of DNA.

Question 10

What happens to the DNA during the SECOND level of condensation?

Answer 10

1. DNA is further folded or coiled to produce the solenoid (30-nm chromatin fibre).
2. Histone H1 and linker DNA is involved in the coiling of the 10-nm nucleosome fibre to produce the solenoid.

Question 11

What happens to the DNA during the THIRD level of condensation?

Answer 11

1. Non-histone chromosomal proteins form a scaffold that is involved in condensing the solenoid into looped domains, forming the 300-nm fibre.
2. In mitotic and meiotic chromosomes, the looped domains themselves coil and fold, further compacting all the chromatin to produce the characteristic metaphase chromosome.
   - Width of one chromatid: 700nm
3. Particular genes always end up located at the same places, indicating that the packing steps are highly specific and precise.

Question 12

What are the roles of condensation?

Answer 12

1. To organise and pack the giant DNA molecules into a more compact structure

[Packing into chromatin]

1. To fit within the cell’s nucleus
2. To prevent the long DNA molecules from getting tangled

[Packing into chromosome during cell division]

1. To facilitate their segregation into daughter nuclei
2. DNA molecules of different chromosome will not be entangled and break during separation at anaphase.

Question 13

How many percent of the DNA sequences in eukaryotic genome are coding regions?

Answer 13

3% (Code for proteins/RNA)

Question 14

What are coding sequences?

Answer 14

[Exons] DNA sequences that carry information correspond to specfic genes (e.g. protein-coding/RNA-coding genes), that is ultimately translated into a functional polypeptide

Question 15

How are heavily used gene products encoded

Answer 15

By multiple copies of genes arranged in repeats, either interspersed or in tandem

Question 16

What are examples of non-coding sequences?

Answer 16

Introns
5' & 3' Untranslated regions (UTRs)
Promoters
Enhancer and Silencer
Replication Origin and Termination
Centromeres and Telomeres

Question 17

What are tandemly repetitive DNA?

Answer 17

DNA sequences in which multiple copies are arranged next to each other

Transcriptionally inactive and may play a structural role in the chromosome

E.g. Centromeres and Telomeres

Question 18

What are moderately repetitive DNA?

Answer 18

DNA sequences that are scattered about the genome

E.g. Promoters, Enhancers, Origins of Replication

Question 19

Structure of Centromere

Answer 19

Repetitive DNA sequence, which is an A-T rich region

Question 20

Function of Centromere

Answer 20

Binds several proteins with high affinity to form the kinetochore, which provides the anchor for the spindle fibres

Essential structural for chromosome segregation during cell division

Question 21

Structure of Telomere

Answer 21

Repetitive DNA sequence, which are typically short, repeated T-G rich sequences

Question 22

Function of Telomere

Answer 22

1. To prevent fusion of the ends of the chromosomes with other DNA molecules
2. To prevent exonucleases from degrading the ends of the linear DNA molecules
3. To prevent the loss of genetic information by acting as a disposable buffer
4. To facilitate replication of the ends of the linear DNA molecules, without loss of the termini
5. To prevent cell cycle arrest/cell death

Question 23

Why do telomeres shorten?

Answer 23

1. Since DNA polymerases assemble DNA only in the 5’ to 3’ direction and need a primer, they cannot complete DNA replication to the 5’ ends of both daughter DNA strands.
2. After the removal of the primer, DNA polymerase cannot fill the gap because there is no 3’ -OH group present as a starting point.
3. After many rounds of cell division and hence replication, chromosomes would become progressively shorter because of the gap left after removal of the primer on the 5’ end of the lagging strand.

Question 24

Roles of Telomere

Answer 24

In germ cells, the end replication problem is overcome by the presence of the telomere, a terminal sequence consiting of repeated DNA sequences. These repeats are added on to the ends of chromosomes by telomerase. The template for telomerase is provided by an RNA molecule within the RNA complex.