The Eukaryotic Genome

Question 1

Why is the amount of proteins that can be encoded for in the human genome not close to the expected number, but is for E.coli?

Answer 1

The human genome is more complex and contains a lot of non-coding DNA/RNA.

Question 2

How many protein coding sequences are in the human genome? What percentage is this of the genome?

Answer 2

30,000. 2%.

Question 3

What does the human genome consist of?

Answer 3

Regulatory sequences, introns (non-coding RNA that is transcribed but not translated). pseudo genes, non-coding RNA (infrastructural RNA, regulatory RNA), repetitive DNA.

Question 4

How does non-coding parts of the genome relate to the evolutionary chain?

Answer 4

As we more up the chain we see more non-coding DNA in the genome.

Question 5

What is the rate of renaturation proportionate to?

Answer 5

Number of times the sequence is present in the genome.

Question 6

What is a repetitive sequence?

Answer 6

Sequences like telomeres which repeat but don’t have enough information to encode for proteins.

Question 7

What is the relation to the complexity of DNA and it’s ability to re-anneal.

Answer 7

Hyperchromic effect and Tm. Simple DNA re-anneals quickly and easily, complex take much longer as all sequences are unique.

Question 8

What are the four classes of eukaryotic genomic DNA?

Answer 8

highly repetitive
moderately repetitive
slightly repetitive
single copy sequences

Question 9

Explain highly repetitive DNA.

Answer 9

Short sequences arranged in repeats - AGCAGCAGC etc…often found clustered around the centromere or telomere.

Question 10

Explain moderately repetitive DNA.

Answer 10

Segments of 100 to several thousand base pairs repeated - groups of genes whose products are needed by cells in large quantities e.g histones, ribosomal and tRNA.

Question 11

Explain slightly repetitive DNA

Answer 11

Most genes in the genome are only represented once. E.g globin family - sometimes clustered together on one chromosome.

Question 12

Explain single copy genes in DNA.

Answer 12

Most of the genes of the organism are single copy genes. Take the longest time to re-anneal and are the ones encoding for proteins.

Question 13

Which genes encode for proteins?

Answer 13

Single copy genes.

Question 14

Why is compaction necessary for genetic information to fit into the nucleus?

Answer 14

Human cell has 3 billion bp of DNA with each having a thickness of 3.4 A - total length of DNA 2m, size of nucleus 10-15 micro metres.

Question 15

What is responsible for packaging genetic information in human cells?

Answer 15

Chromosomes.

Question 16

What are the features of a chromosome?

Answer 16

Physical card 17

Question 17

What is chromosome banding?

Answer 17

Chromosomes can be stained with dyes which give a unique pattern for each chromosome so that the bands can be numbered.

Question 18

What is the most common stain used for chromosome banding and how is it used?

Answer 18

Giemsa stain. When applied after mild proteolytic treatment gives a light and dark band pattern.

Question 19

What is chromatin?

Answer 19

The genetic material which makes up the chromosomes - composed of DNA and protein.

Question 20

What is heterochromatin?

Answer 20

Tightly packaged - isn’t transcribing much.

Question 21

What is euchromatin?

Answer 21

Euchromatin contains most active genes; actively transcribed.

Question 22

How much DNA does each chromosome contain?

Answer 22

A single molecule of DNA.

Question 23

DNA is wound around ______ called ______.

Answer 23

Small proteins. Histones.

Question 24

Histone proteins have a ____ charge. This allows for association with the ______.

Answer 24

Positive. Negatively charged backbone.

Question 25

What is a histone octamer? How is it formed? What is the resulting structure?

Answer 25

Physical card 37

Question 26

What is the major force holding the association of histones to DNA?

Answer 26

Electrostatic.

Question 27

How can DNA and histones be separated?

Answer 27

Take advantage of electrostatic bond. Chromatin treated with high ionic strength solutions to reduce electrostatic interactions and protein dissociates from the DNA.

Question 28

What is the role of histones?

Answer 28

Shield negative charges of phosphates.
Allow bending and DNA wrapping.
Restrict access to transcription.

Question 29

What is histone remodelling?

Answer 29

Influences DNA accessibility for transcription.

Question 30

What are the ways in which histones can be modified?

Answer 30

Phosphorylation
Methylation
Acetylation

Question 31

What is Acetylation?

Answer 31

Transferring an acetyl group to the amino acid chain of lysine residues.

Question 32

What do histone acetyl transferases do?

Answer 32

Histone acetyl transferases (HATs) add acetyl groups, neutralise the lysine positive charge and weaken the electrostatic interactions between phosphates from DNA and histones - loosen the packaging - allows for increased gene expression.

Question 33

What do histone deacetylases (HDACs) do?

Answer 33

Remove acetyl groups, enhance electrostatic interactions and tighten packaging.

Question 34

What is the mechanism by which HATs perform?

Answer 34

Associated with transcriptional co-activators - relaxes chromatin and provides binding sites for proteins that stimulate transcription.