Lecture 2 - Components Of Higher Eukaryotic Genomes

Question 1

Does Genome size correlate with complexity of species?

Answer 1

No

Question 2

What is the C value paradox?

Answer 2

The idea that bigger genome = more complex organ but this is not true

Question 3

Does the number of gene significantly increase with the size of genomes?

Answer 3

No

Question 4

Does most of the genome encode protein?

Answer 4

No

Question 5

What do CoT renaturation curves measure?

Answer 5

DNA reassociation kinetics measuring the rate by which heat denatured DNA will renature in a solution

Question 6

In CoT renaturation will all heat-denatured DNA re-associate?

Answer 6

Yes

Question 7

CoT renaturation - what is the rate at which DNA sequences re-associate proportional to?

Answer 7

The number of copies of the sequence found in the genome

Question 8

What does CoT value depend on?

Answer 8

DNA concentration, Rex association temperature, cation concentration and viscosity

Question 9

What is the CoT equation?

Answer 9

Co x t x buffer factor

Co - initial concentration of DNA (mol/L)
t - renaturation time (sec)
buffer factor - the effects of cations and the speed of renaturation

Question 10

What would renature at a lower CoT factor - a single copy sequence or a repetitive DNA sequence?

Answer 10

Repetitive DNA sequences

Question 11

How much of the genome is receptive DNA?

Answer 11

70%

Question 12

What is the encyclopaedia of DNA elements?

Answer 12

ENCODE

Question 13

What is the genome made up of?

Answer 13

1.5% - protein coding
26% - non-coding introns
The rest is competitive sequences

Question 14

What are transcribed in RNA?

Answer 14

Exons and introns

Question 15

What are spliced out to get mature RNA?

Answer 15

Introns

Question 16

What are promotor regions rich in and what do they have?

Answer 16

GC rich and CPG island

Question 17

Where are genes more concentrated about?

Answer 17

In GC region

Question 18

What reveals the distribution of CPG islands?

Answer 18

FISH

Question 19

What side are CPG islands found on?

Answer 19

Left side

Question 20

Are centromere GC poor?

Answer 20

Yes

Question 21

Do all chromosomes have the same GC content?

Answer 21

No

Question 22

What are CPG islands?

Answer 22

Short stretches of palindromic DNA that encodes the same sequence in the complementary strand.

Question 23

What are repetitve sequences?

Answer 23

Sequence present more than one coy per haploid genome

Question 24

What are the 3 different types of repeats?

Answer 24

Gene families - arise from fixed segmental duplications
Interspersed repeats
Tandem repeats

Question 25

After being fixed and duplication genes with go through different fates - one of these is pseudogenization. What is this?

Answer 25

The duplication gene is made inactive and is invisible to natural selection

Question 26

After being fixed and duplicated genes will go through different fates - one of these is neofunctionslization. What is this?

Answer 26

A new function is evolved

Question 27

After being fixed and duplicated genes will go through different fates - one of these is subfunctionalization. What is this?

Answer 27

A duplication occurs in the regulatory elements of the gene which means that two genes need to function together and are independent in one another.

Question 28

What is an example of a gene family?

Answer 28

Haemoglobin cluster - these have different forms in fetuses

Question 29

Another example of a gene family amplify signals by making lots of duplicated repeated units. What is this family?

Answer 29

His tones

Question 30

In his tones where are his tone gene clusters found?

Answer 30

At 4 discrete lock

Question 31

What are interspersed repeats.

Answer 31

Dispersed throughout the genome

Question 32

What are the two type of interspersed repeats?

Answer 32

LINES and SINE’s

Question 33

Where are SINE’s found?

Answer 33

Within and between genes

Question 34

What can be used as markets of SINE’s

Answer 34

Alu repeats

Question 35

What have SINE’s and LINE’s integrated using?

Answer 35

Reverse transcriptase

Question 36

How do SINEs and LINEs enter the genome?

Answer 36

Transcribed into RNA then reverse transcribed into DNA before entering genome

Question 37

What incomes reverse transcriptase?

Answer 37

Active LINE

Question 38

Are interspersed repeats commonly suppressed? And why is this good?

Answer 38

Repeats can come from anywhere and insert anywhere which is why it’s good they are commonly suppressed

Question 39

In what situation and why would interspersed repeats he dangerous?

Answer 39

If they insert into coding regions they can disrupt function

Question 40

Can interspersed repeats cause genome rearrangements?

Answer 40

Yes

Question 41

What disease does three line insertions into chromosomes 22 cause?

Answer 41

Severe haemophilia A

Question 42

What are variable tandem repeats?

Answer 42

Repeats which are dispersed throughout the genome and repeated in tandem

Question 43

What are the three types of satellites?

Answer 43

satellite Minisatellite Microsatellite (TTAGGG)

Question 44

What are VNTRs variable in number?

Answer 44

Unequal crossing over - when recombined they might duplicate or delete DNA replication slippage - backwards = dna falls backwards and insertion happens Forward = lagging strand jumps causing deletion DNA repair adds the tandem repeats

Question 45

Is repeat number inherited?

Answer 45

Yes

Question 46

Are repeat numbers stable?

Answer 46

No

Question 47

What can unstable repeat numbers cause?

Answer 47

Triplet numbers vary and can cause disease

Question 48

How can Microsatellite VNTR’s get worse with each generation inherited?

Answer 48

Someone will pass on mutated VNTRS and then their offspring could also have their own VNTRs meaning the offspring have more than the parents did and will get the dues ease earlier than the parents will

Question 49

What are minisatelites?

Answer 49

Small sequences of dna that don’t encode protein and appear throughout the genome hundreds of times

Question 50

Are the number of repeats reliably inherited?

Answer 50

Yes

Question 51

How does dna fingerprinting work?

Answer 51

Digest dna into small fragments using restriction enzymes and run the fragments with minisatelites on a gel. Southern blot them and then incubate with radioactive dna proves or fluorescence to get a fingerprint

Question 52

Can you amplify minisatelites?

Answer 52

Yes but it’s hard as you need to design primers right down the region

Question 53

How can you get a fingerprint from a small region of dna minisatelites in evidence?

Answer 53

PCR amplification then separate using gel electrophoresis and then create histograms to compare size of fragments Currently they use short tandem repeats (STR’s)