Lecture 2: Components Of Higher Eukaryotic Genomes

Question 1

What does the c-value paradox explain?

Answer 1

Genome size is not equal to genome complexity

Question 2

What influences Cot value?

Answer 2

DNA concentration, translocation temperature, cation concentration, and viscosity

Question 3

What is the Cot equation?

Answer 3

Co x t x buffer factor

Co = initial DNA concentration (mol/l)
t = renaturation time (sec)
Buffer factor = accounts for affect of cations on the speed of renaturation

Question 4

What’s the purpose of Cot renaturation curves?

Answer 4

To determine genome complexity

Question 5

What does a lower Cot value indicate?

Answer 5

DNA is more abundant and repetitive

Question 6

What do protein coding genes contain?

Answer 6

~25kb consisting of introns and exons to be transcribed into RNA

Question 7

What changes are made to protein coding gene to for mature mRNA?

Answer 7

• introns are spliced out
• no CpG island
• still contains exons and 5’ and 3’ untranslatable regions

Question 8

How large is the genes translatable coding sequence and what does this tell us?

Answer 8

1.3kb, much less than 25kb
Shows that most of the unique parts of a gene are actually non coding

Question 9

What are gene families?

Answer 9

Genes present in more than 1 copy per haploid genome which arise by duplication

Question 10

What are the 3 different dates of duplicated genes?

Answer 10

Pseudogenization: gene inactivation
Neofunctionalization: evolution of a new function
Subfunctionalization: function is divided between genes

Question 11

What is the difference between win structure between adult and foetal haemoglobin?

Answer 11

Adult subunits - 2 alpha and 2 beta
Foetal subunits - 2 alpha and 2 gamma

Question 12

Where are haemoglobin subunits found?

Answer 12

Alpha subunits - tip of short arm of chromosome 16
Beta, gamma, and delta subunits - chromosome 11

Question 13

Where is the largest histone gene cluster found in humans?

Answer 13

Chromosome 6

Question 14

Why is it beneficial to have so many histone repeats?

Answer 14

Histones are important for DNA packaging, so lots of proteins are needed to carry out the function quickly

Question 15

What are interspersed repeats?

Answer 15

Repeats dispersed throughout the genome, non adjacent to eachother

Question 16

What are SINEs? How large are they and which is most abundant?

Answer 16

Short interspersed nuclear elements
100-300bp
Alu is most abundant, 11% of genome

Question 17

What are LINEs? How large are they and which is most abundant?

Answer 17

Long interspersed repeats
1-5kb
Li is most abundant, 17% of genome

Question 18

How do interspersed repeats use reverse transcription to spread?

Answer 18

Active LINEs encode reverse transcriptase, which then transposes themselves and SINEs to integrate

Question 19

What causes the intron 22 inversion mutation of the F8 gene?

Answer 19

3 LINE insertions

Question 20

What are VNTRs?

Answer 20

Variable number tandem repeats which are dispersed throughout the genome and are short sequences repeated multiple times in tandem

Question 21

What are the 3 groups of VNTRs and their sizes?

Answer 21

Satellite DNA: >100bp located in centromere (AT rich)
Minisatellite DNA: 15-100bp
Microsatellite DNA: <15bp

Question 22

Why is the important micrsatellite DNA found in telomeres?

Answer 22

Hexameric sequence TTAGGG

Question 23

Why are VNTRs variable in number?

Answer 23

• unequal crossing over
• DNA replication slippage
• DNA repair
• repeat number is inherited through pedigrees

Question 24

What causes triplet repeat diseases?

Answer 24

Length variation in specific microsatellites, as expansion beyond a threshold results in morphological disease

Question 25

What are the steps involved in DNA fingerprinting?

Answer 25

• genomic DNA is extracted from biological sample
• DNA is digested into small fragments by restriction enzymes
• some fragments contain mini satellites of interest
• electrophoresis separates fragments by size
• transferred to membrane using southern blot
• membrane is incubated with fluorescent DNA probes and hybridize with complementary fragments
• results show pattern of bands on gel

Question 26

What do probes of minisatellite sequences detect?

Answer 26

Polymorphic patterns of restriction endonuclease fragments

Question 27

How can genetic fingerprints be generated using multiple microsatellite VNTRs

Answer 27

• specific parts of DNA are put though PCR with PCR primers
• amplifies different microsatellites which are labelled with coloured fluorophores
• labelled DNA fragments are generated and separated with electrophoresis

Question 28

What is genetic fingerprinting used for?

Answer 28

Paternity tests, forensics, identifying diseases and wildlife conservation studies