Lecture 28 - Genes and genomes Flashcards
Major problem with lagging strand mechanism
Chromosomes get shorter after each replication : 5’ ends of replicated DNA (daughter strands) are not complete
Solution to incomplete replication (lagging strand mech)
enzyme telomerase
In what cells telomerase enzyme is active (3 types)
Germ cells (embryonic cell with potential to become a gamete), stem cells and cancer cells
Link of number of cell divisons with amount of telomerase -> which cell type does not divide much due to that
More telomerase = can do more cell divisions. Somatic cells don’t do much because of that
Mice missing telomerase gene consequence
OK for 3 generations and then fecundity declines
Repeated sequence of DNA in telomeres in Tetrahymena (where telomerase discovered) and in humans
Tetrahymena : TTGGGG
Humans : TTAGGG
What kind of protein telomerase is and what these are
Reverse transcriptase : DNAPs that use RNA as a template
What is particular about telomerase
Carries its own template RNA complementary to the tel sequence
3 steps of telomerase action (that are repeated multiple times)
Elongation, Translocation (movement towards the 3’ end of the extended strand), Elongation
Why telomerase extends the 3’ strands
To give primase (RNAP primase) more DNA to primer on, so 5’ end can be completed
What organism telomerase and telomeric sequences were identified in
ciliated protist tetrahymena, a unicellular eukaryote
something particular about tetrahymena’s nucleus
Has a micronucleus with original genome (transcriptionally inactive)
Has a macronucleus with millious of gene sized DNA pieces (transcriptionally active)
3 species in order of DNA content/gene number
Prokaryote (bacteria), Simple eukaryote (yeast), Complex eukaryote (man)
With genome evolution, what varies more dramatically ? DNA content or gene number
DNA content
3 things to consider for explaining why DNA content varies more dramatically than gene number in genomic evolution
Distance between genes, genes length, introns number and length
Gene size, introns/gene ratio and % of gene length that are introns in YEAST
1.6 kb / gene , 0.05 introns / gene, 1 % introns
Gene size, introns/gene ratio and % of gene length that are introns in HUMAN
50 kb / gene , 8 introns / gene, 95 % introns
Why yeast would prefer more ‘‘gene concentrated’’ genome (2)
1) has to do a lot of replication when in presence of nutrients
2) Most of its energy is spent on replication
4 things/elements found in human genome + % they represent
Mobile elements : 45%, Repetitive sequences : 50%, Genes : 55%, Tandem repeats : 5%
What are TRs + what they do
Tandem repeats : consecutive repeats of DNA sequences that code for functional RNAs (and not proteins)
% of total human genome that is protein-coding regions
Approx 1.2%
Def. of simple sequence DNAs
direct repeats of 3-50 bases.
Where simple sequence DNAs may be found (3)
Telomeres, centromeres, within genes
How simple sequence DNAs are related to some human genetic diseases
Simple sequence is within a gene and expands -> becomes toxic (ONLY IF IN GENE)
Ex. of disease due to simple sequences DNAs expanding in genes
Huntington disease : trinucleotide repeat of CAG expands
How expansion simple sequence DNAs happens
splippage to form a loop during replication due to thermal energy -> one daughter DNA contains an extra repeat of the sequence
How southern blot helps detecting number of repeats of a simple sequence DNA
The more the fragment migrated, the less it has repeats of a simple sequence DNA (probe of simple sequence DNA used) Size of fragments depends on number of repeats it has
Why southern blotting of DNA fragments with simple sequence DNA gives diff. results from one person to another
Each person has a different number of the simple sequence DNA found at each site where it is present (polymorphism)
MEDIRs distribution, length, number and genome %
Mobile element-derived interspersed repeats.
Interspersed, 100 - 10k bps, more than 1M copies, 45% of human genome
MEDIRs what is the consequence of the fact that they can move
Can increase in number over evolutionary time
MEDIRs their function for the organism + nickname
No function for the organism : ‘‘Selfish DNA’’
what is a germ line
germ cells that come from earlier germ cells
Frequency of germ line element transposition events
1 germ line transposition (out of the >1M MEDIRs) in one person in 8 (compared with their parents)
2 major classes of MEDIRs and what differentiates them
1) DNA transposons
2) Retrotransposons
Different by their mechanism of transposition
DNA transposons how transposition works
Direct transposition at DNA level.
DNA transposons : what is the participating enzyme + where it comes from ?
Participating enzyme = transposase (ENCODED IN THE ELEMENT ITSELF)
Retrotransposons how transposition works
Indirect transposition via an RNA intermediate
Retrotransposition : what is the participating enzyme (2) + where it comes from ?
RNAP (cellular), Reverse transcriptase (encoded in the element itself)
DNA transposons 2 steps mechanism
1) Transposase takes off transposon (from DONOR DNA) and join adjacent non-transposon regions together
2) DNA tranposon inserted elsewhere in the DNA (TARGET DNA)
2 recognizable sites before and after MEDIRs transposition
Former transposon site and Insertion site
3 steps mechanism of retrotransposons transposition
1) Retrotransposon is transcribed by RNAP
2) RNA intermediate converted to DNA (a copy of the transposon ! ) by a reverse transcriptase (ENCODED IN THE TRANSPOSON ITSELF)
3) retrotransposon copy (DNA intermediate) inserted elsewhere
Cut and paste transposition during DNA replication consequence/what MEDIR is concerned
increase of genomic copy number of DNA tranposons
Cut and paste transposition 3 steps
1) ‘‘Before S phase’’ DNA contains one copy of transposon
2) During replication, after transposon is replicated on two daughter strands, it jumps to non replicated sequence
3) One daughter strand has a copy and the other has two copies
What viruses retrotransposons are related to
retroviruses like AIDS virus HIV
(3) Major classes of retrotransposons in the human genome
LTR elements
LINEs
SINEs
What LTR elements are
(retrotransposons) contain Long Terminal Repeats, like retroviruses
What LINEs are + length + something particular they do
(retrotransposons) Long Interspersed Elements 1 to 6 kb
Code for proteins involved in their own retrotransposition
What SINEs are + length + why considered parasites for LINEs
(retrotransposons) Short Interspersed, 300 bp, do not encode proteins but may use LINE-encoded proteins
When accumulation of mobile elements is a problem and when it is not
Problem if happens within genes. If outside genes, makes no difference
What happens to mobile elements over time (once copied/pasted)
Accumulate mutations and differ more and more of their parent molecule and their sibling molecule.
What most of the non-repetitive non-coding DNA in the human genome is thought to be
Ancient mobile elements that undercame so many mutations that their ressemblance is not recognizable
Important distinction between DNA transposons and retrotransposons IN TRANSPOSITION
DNA transposons : changes place (0 new copies)
Retrotransposons : Makes a copy that goes somewhere else (1 new copy)
Important distinction between DNA transposons and retrotransposons IN THEIR INCREASE IN NUMBER
DNA transposons : Increase in number happens because of transposition during replication
Retrotransposons : Increase in number because they make A COPY that goes to a target site
