Lecture 2 - Components Of Higher Eukaryotic Genomes Flashcards
Does Genome size correlate with complexity of species?
No
What is the C value paradox?
The idea that bigger genome = more complex organ but this is not true
Does the number of gene significantly increase with the size of genomes?
No
Does most of the genome encode protein?
No
What do CoT renaturation curves measure?
DNA reassociation kinetics measuring the rate by which heat denatured DNA will renature in a solution
In CoT renaturation will all heat-denatured DNA re-associate?
Yes
CoT renaturation - what is the rate at which DNA sequences re-associate proportional to?
The number of copies of the sequence found in the genome
What does CoT value depend on?
DNA concentration, Rex association temperature, cation concentration and viscosity
What is the CoT equation?
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
What would renature at a lower CoT factor - a single copy sequence or a repetitive DNA sequence?
Repetitive DNA sequences
How much of the genome is receptive DNA?
70%
What is the encyclopaedia of DNA elements?
ENCODE
What is the genome made up of?
1.5% - protein coding
26% - non-coding introns
The rest is competitive sequences
What are transcribed in RNA?
Exons and introns
What are spliced out to get mature RNA?
Introns
What are promotor regions rich in and what do they have?
GC rich and CPG island
Where are genes more concentrated about?
In GC region
What reveals the distribution of CPG islands?
FISH
What side are CPG islands found on?
Left side
Are centromere GC poor?
Yes
Do all chromosomes have the same GC content?
No
What are CPG islands?
Short stretches of palindromic DNA that encodes the same sequence in the complementary strand.
What are repetitve sequences?
Sequence present more than one coy per haploid genome
What are the 3 different types of repeats?
Gene families - arise from fixed segmental duplications
Interspersed repeats
Tandem repeats
After being fixed and duplication genes with go through different fates - one of these is pseudogenization. What is this?
The duplication gene is made inactive and is invisible to natural selection
After being fixed and duplicated genes will go through different fates - one of these is neofunctionslization. What is this?
A new function is evolved
After being fixed and duplicated genes will go through different fates - one of these is subfunctionalization. What is this?
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.
What is an example of a gene family?
Haemoglobin cluster - these have different forms in fetuses
Another example of a gene family amplify signals by making lots of duplicated repeated units. What is this family?
His tones
In his tones where are his tone gene clusters found?
At 4 discrete lock
What are interspersed repeats.
Dispersed throughout the genome
What are the two type of interspersed repeats?
LINES and SINE’s
Where are SINE’s found?
Within and between genes
What can be used as markets of SINE’s
Alu repeats
What have SINE’s and LINE’s integrated using?
Reverse transcriptase
How do SINEs and LINEs enter the genome?
Transcribed into RNA then reverse transcribed into DNA before entering genome
What incomes reverse transcriptase?
Active LINE
Are interspersed repeats commonly suppressed? And why is this good?
Repeats can come from anywhere and insert anywhere which is why it’s good they are commonly suppressed
In what situation and why would interspersed repeats he dangerous?
If they insert into coding regions they can disrupt function
Can interspersed repeats cause genome rearrangements?
Yes
What disease does three line insertions into chromosomes 22 cause?
Severe haemophilia A
What are variable tandem repeats?
Repeats which are dispersed throughout the genome and repeated in tandem
What are the three types of satellites?
satellite
Minisatellite
Microsatellite (TTAGGG)
What are VNTRs variable in number?
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
Is repeat number inherited?
Yes
Are repeat numbers stable?
No
What can unstable repeat numbers cause?
Triplet numbers vary and can cause disease
How can Microsatellite VNTR’s get worse with each generation inherited?
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
What are minisatelites?
Small sequences of dna that don’t encode protein and appear throughout the genome hundreds of times
Are the number of repeats reliably inherited?
Yes
How does dna fingerprinting work?
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
Can you amplify minisatelites?
Yes but it’s hard as you need to design primers right down the region
How can you get a fingerprint from a small region of dna minisatelites in evidence?
PCR amplification then separate using gel electrophoresis and then create histograms to compare size of fragments
Currently they use short tandem repeats (STR’s)
