S3: Chromosome Structure and Function

Question 1

What does it mean that chromosomes are not functionally discrete?

Answer 1

This means that organisms often have different numbers of chromosomes even if they are of similar complexity. Some less complex organisms can have many more chromosomes, so chromosomes does not equate to complexity.

Question 2

What is synteny? Describe it

Answer 2

Synteny means from the same thread and it is studied in comparative genomics.

• Genes do not necessarily have to be retained on the same chromosomes e.g. DNA in human chromosome 1 have been rearranged and spread among many chromosomes in mice.
• Chromosomes are there to keep DNA in a safe way to be passed on.

Question 3

What phase does DNA replicate in the cell cycle?

Answer 3

The DNA replicates during interphase, during S phase (G1-S-G2-PMAT).

Question 4

Describe structure of metaphase chromosome

Answer 4

• Short arm (p arm) and a long arm (q arm) and this is because the centromere is never quite in the middle of the chromosomes. The sizes of arms vary and this is one of the identifying features of different chromosomes.
• The centromere holds the sister chromatids together.
• The telomere is the bit at the end of the chromosome.
• Bands of the chromosomes are due to staining and help identify the chromosomes.

Question 5

3 functionally discrete elements of chromosomes

Answer 5

1. The centromere (the middle).
2. The telomeres (the ends).
3. Origins of replication (multiple copies).

Question 6

Describe structure of centromere in humans

Answer 6

• In humans, our centromeres are very complicated.
• They are megabases made up of repetitive DNA and the major component is the alpha satellite DNA in humans.
• All chromosomes have different satellite DNA configuration. These are very long pieces of DNA that are hard to study as restriction enzymes cut them into too long pieces of DNA which are fragile and break.

Question 7

Function of the centromere

Answer 7

One of the main functions of the centromere which is to keep the sister chromatids joined until metaphase.

Question 8

Describe the role of spindles and centromere during metaphase and anaphase

Answer 8

Spindles align the chromosomes down the metaphase plate. the centromere allows the sister chromatids to bind to the mitotic spindle. Special proteins bind and form a kinetochore where the spindles bind (attachment site for chromosomes to mitotic spindle). During anaphase, the sister chromatids then get pulled to opposite poles of the cell, allowing each cell to have the same pairs of chromosomes.

Question 9

What are telomeres?

Answer 9

They are on the end of chromosomes and made up of a tandem repeat (TTAGGG in humans). It is an overhang of single stranded region. They stop the DNA from falling apart and fraying in DNA.

Question 10

What is the hayflick limit?

Answer 10

This is the number of times a cell can divide before it dies. This is because eventually genome will be lost as the overhang keeps decreasing in length with replication.

Question 11

Describe the Telomere End Replication Problem

Answer 11

In DNA replication, there is a leading strand that is continuous because it is going in the 5’-3’direction. The other strand is called the lagging strand, because it has to keep restarting replication, with primers having to be laid down each time. Therefore it forms lots of fragments called okazaki fragments. Remember that DNA replication only occurs in the 5’-3’direction. so there are bidirectional origins of replication. Also, DNA polymerase needs a primer for the lagging strand.

• The primers then have to be removed and the fragments are ligated, however the cell is unable to fill in the very end of the chromosome so the new DNA formed is shorter. If this was the mechanism, then with many rounds of replication the chromosomes would get shorter and shorter. Eventually it would hit a gene and things would start getting messed up and the cell would die.
• Telomeres help with the end replication problem.

Question 12

How do telomeres help with the end replication problem?

Answer 12

The telomere at the end of the chromosome is repetitive DNA, so there is a lot of this DNA present until any meaningful DNA is reached.
Hence it would take quite a while of shortening to reach it!
However, eventually you would run out, for example germ cells that have to pass on the chromosomes to offspring so there is another mechanism of telomerase which prevents genome being lost during replication.

Question 13

How do telomerase help with the end replication problem?

Answer 13

Certain cell types can continue to divide because they express an enzyme called telomerase. Expression of this enzyme is regulated during development and they are often found to be expressed in cancer cells.
- Telomerase enzyme extends the DNA so the original length of the DNA is restored.

Question 14

Describe the mechanism of telomerase

Answer 14

The telomerase enzyme is an enzyme made up of protein and some RNA ( a RNA dependent DNA polymerase that adds telomeric DNA to telomeres)! The enzyme comes along and as the RNA sequence is complementary to the telomere repeat, it allows to increase the length of the DNA.
Once the DNA is lengthened, another primer will be put on that will allow to prime in the 5’-3’ direction and restore the original sequence that would have been there previously.
This prevents the shortening of DNA/chromosomes during replication and subsequent cell division.

Question 15

What cells have or don’t have telomerase?

Answer 15

Embryonic stem cells and germ cells have active telomerase because they need it - especially germ cells due to offspring.
However somatic cells do not have telomerase. The telomere length drops with number of cell divisions. For example if we had skin cells and grew them in a dish, they would divide for about 30 and then stop dividing and die. This is called the hayflick limit.

Question 16

How is the telomere and telomerase important clinically?

Answer 16

• Telomere length is useful for determining age in forensic samples.
• Shortening of telomerase is associated with cellular senescence (aging)
• Cancerous cells reactivate telomerase

Question 17

What is the origin of replication?

Answer 17

DNA synthesis begins at replication origin.
Bacteria have a single replication origin because they don’t have that many base pairs, however eukaryotic chromosomes are large and DNA replication is slower, so multiple replication origins must fire simultaneously for replication to be completed within a reasonable time scale.

Question 18

How is DNA highly folded in an organised way?

Answer 18

It uses histones to do this.

Question 19

What are histones?

Answer 19

The major protein component of a chromosome is histones, they are small, highly basic and highly conserved. We have 5 main types: Histone H1, H2A, H2B, H3, H4.

Question 20

Why do histone’s self assemble into a octamer core?

Answer 20

A histone has two functional areas:
- One are is highly basic having lots of lysing and arginine. These amino acids are postively charged at out bodies pH.
- The other end is highly hydrophobic which makes it want to clump together and form a ball.
When they self assemble, they are like a ball, but they still have the bristly bits sticking out when they are the octamer.

Question 21

Why can the DNA wrap around the histone octamer to form a nucleosome?

Answer 21

Because the tails of the histone octamer are positively charged and the DNA sugar-phosphate backbone is negatively charged they attract one another.

Question 22

What is ‘beads on string’’?

Answer 22

When the DNA binds to numerous of these histones, you get a nucleosome array, also referred to as beads on a string as this is what it appears like under microscope. A nucleosome is good for storing and packing DNA.

Question 23

What are dinucleosomes?

Answer 23

Nucleosomes linked by histone 1. Because of this, the nucleosomes can adopt a higher level of folding. They can compact together to form a 30nm chromatin fibre.
There is even higher folding, like chromatin loops with scaffold.

Question 24

What are the two types of extreme chromatin?

Answer 24

• There are extremes in chromatin compaction, the extremely compact form of chromatin is called heterochromatin. Centromeres are made of heterochromatin and are very tightly packaged.
• The opposite to that is euchromatin which is less condensed/tightly packaged. Genes tend to be in the euchromatic parts of the genome.
• Euchromatin is light in colour on staining whereas the heterochromatin stains dark.

Question 25

How can heterochromatin be constutive or faculative?

Answer 25

Heterochromatin can be constitutive, meaning it’s pretty much in every cell, such as the centromeres.
Or it can be facultative, which is that some parts of the genome may be tightly packaged in one cell type because it isn’t really expressed, but in another cell type it is less tightly packaged because it needs to be opened up.

Question 26

When in the cell cycle is chromosome compaction highest?

Answer 26

Chromosome compaction is highest during mitosis/meiosis. This is because if we have very long chromosomes then during metaphase they would tangle.

Question 27

What is chromosome territory?

Answer 27

During interphase, chromosomes tend to occupy a spatially limited space called a chromosome territory.

Question 28

How does DNA methylation have a large impact on the regulation of gene expression?

Answer 28

• The cytosine in CpG dinucleotides can be methylated.
• DNA methylation is associated with stable long term repression.
• DNA methylation is established in the embryo

Question 29

List some histone modifications

Answer 29

The influence on chromatin structure and gene function differs depending on the type and location of the modification 
	• Acetylation
	• Methylation
	• Phosphorylation
	 • ubiquitylation