Genome organisation

Question 1

How much of the human genome codes for proteins?

Answer 1

Less than 5%.

Question 2

Single celled prokaryote gene content?

Answer 2

Densely packed with genes, few introns.

Question 3

Define metazoa?

Answer 3

All animals other than protozoans and sponges. Multicellular animals with differentiated tissues.

Question 4

Define protozoa?

Answer 4

All the single celled microscopic animals, including amoebas, flagellates, ciliates, sporozoans.

Question 5

Metazoan gene content?

Answer 5

Less gene rich, with introns and repetitive elements.

Question 6

What is coding DNA used for?

Answer 6

Mostly used to make mRNA and then polypeptides. Some specifies untranslated RNA (non-coding RNAs).

Question 7

How are genes organised (prokaryotes and eukaryotes)?

Answer 7

Prokaryotes are poly-cistronic with one mRNA being produced for several genes, controlled by one operon.
Eukaryotes are mon-cistronic with one mRNA for one gene, however, can get eukaryotic operons where genes are co-expressed.

Question 8

Types of non-coding DNA?

Answer 8

1. Tandemly repeated DNA (satellite DNA)

2. Interspersed genome wide repeats includes LINES, SINES, LTR transposons, and DNA transposons.

Question 9

Describe tandemly repeated DNA?

Answer 9

Most have no apparent function. Between 2-20 000 nucleotides repeated.
Mechanism of origin is likely to be different for short compared to long repeats.
-short: random changes in non-functional sequence
-long: duplicate by crossing over
DNA fingerprinting makes use of these repeats

Question 10

Does tandemly repeated DNA have any important functions?

Answer 10

Yes in centromeres and telomeres

• alphoid is found in the human genome around centromeres, and is retained by selection due to being the site of interaction with the spindle fibres in mitosis/meiosis.
• telomeres are important to prevent the loss of genes during replication.

Question 11

What are the different types of interspersed genome-wide repeats?

Answer 11

Derived from transposable elements. Most complex genomes contain inactive integrated pro-viral elements which behave as selfish elements.
Mobile DNA sequences which can migrate to different regions of the genome.
Only a tiny majority are actively transposing, most are relics and cannot move/increase in numbers.
1. LINES – Long Interspersed Elements
2. SINES – Short Interspersed Elements
3. LTRs – Long Terminal Repeat Retrotransposons
4. DNA transposons

Question 12

Describe LINES?

Answer 12

Autonomous retrotransposons derived from selfish DNA sequence encoding reverse transcriptase. Very ancient, but makes up 21% of the human genome. 1% are still capable of transposition. Occasionally cause disease by disrupting gene function

Question 13

Describe SINES?

Answer 13

Don’t encode their own reverse transcriptase. 13% of the human genome. Disperse via an RNA intermediate which undergoes reverse transcriptase, therefore relies on reverse transcriptase being produced elsewhere. Non-autonomous.

Question 14

Describe LTR transposons?

Answer 14

Highly related to retroviruses. More common than DNA transposons. Not normally capable of further proliferation.

Question 15

Describe DNA transposons?

Answer 15

Transpose in a more direct DNA to DNA manner. Encode a transposase which cuts the transposon from the chromosome and catalyses its reinsertion at other chromosomal locations. May be autonomous or non-autonomous.

Question 16

Example of an active LINE?

Answer 16

Insertion of LINEs into factor VIII causes haemophilia A.

Question 17

What is the c value paradox?

Answer 17

Genome size doesn’t correlate well with complexity/gene number in eukaryotes.

Large genomes are largely transposable elements so genome size generally correlates with number of transposable element sequences rather than gene content.

Question 18

What does a successful transposable element do?

Answer 18

Increase copy number without harming its host, which can be done by targeting safe havens – regions of the genome where there are few genes.

Question 19

How can unequal crossing over occur?

Answer 19

Homologous elements located close together will catalyse unequal crossing over, leading to duplication of genes located between homologous elements. Can miss out a gene or lead to duplication, allowing the copy to accumulate mutations as the first can do the work. This can lead to an improved version then selection occurs for genome evolution. Can also lead to pseudogenes or gene fragments.

Question 20

How can genome size increase?

Answer 20

Exons may duplicate or shuffle around
Genes duplicate or create gene families
Gene families duplicate to produce gene super-families
Entire genome can duplicate