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Biol 200 > Lecture 28 - Genes and genomes > Flashcards

Lecture 28 - Genes and genomes Flashcards

1
Q

Major problem with lagging strand mechanism

A

Chromosomes get shorter after each replication : 5’ ends of replicated DNA (daughter strands) are not complete

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2
Q

Solution to incomplete replication (lagging strand mech)

A

enzyme telomerase

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3
Q

In what cells telomerase enzyme is active (3 types)

A

Germ cells (embryonic cell with potential to become a gamete), stem cells and cancer cells

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4
Q

Link of number of cell divisons with amount of telomerase -> which cell type does not divide much due to that

A

More telomerase = can do more cell divisions. Somatic cells don’t do much because of that

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5
Q

Mice missing telomerase gene consequence

A

OK for 3 generations and then fecundity declines

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6
Q

Repeated sequence of DNA in telomeres in Tetrahymena (where telomerase discovered) and in humans

A

Tetrahymena : TTGGGG

Humans : TTAGGG

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7
Q

What kind of protein telomerase is and what these are

A

Reverse transcriptase : DNAPs that use RNA as a template

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8
Q

What is particular about telomerase

A

Carries its own template RNA complementary to the tel sequence

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9
Q

3 steps of telomerase action (that are repeated multiple times)

A

Elongation, Translocation (movement towards the 3’ end of the extended strand), Elongation

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10
Q

Why telomerase extends the 3’ strands

A

To give primase (RNAP primase) more DNA to primer on, so 5’ end can be completed

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11
Q

What organism telomerase and telomeric sequences were identified in

A

ciliated protist tetrahymena, a unicellular eukaryote

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12
Q

something particular about tetrahymena’s nucleus

A

Has a micronucleus with original genome (transcriptionally inactive)
Has a macronucleus with millious of gene sized DNA pieces (transcriptionally active)

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13
Q

3 species in order of DNA content/gene number

A

Prokaryote (bacteria), Simple eukaryote (yeast), Complex eukaryote (man)

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14
Q

With genome evolution, what varies more dramatically ? DNA content or gene number

A

DNA content

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15
Q

3 things to consider for explaining why DNA content varies more dramatically than gene number in genomic evolution

A

Distance between genes, genes length, introns number and length

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16
Q

Gene size, introns/gene ratio and % of gene length that are introns in YEAST

A

1.6 kb / gene , 0.05 introns / gene, 1 % introns

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17
Q

Gene size, introns/gene ratio and % of gene length that are introns in HUMAN

A

50 kb / gene , 8 introns / gene, 95 % introns

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18
Q

Why yeast would prefer more ‘‘gene concentrated’’ genome (2)

A

1) has to do a lot of replication when in presence of nutrients
2) Most of its energy is spent on replication

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19
Q

4 things/elements found in human genome + % they represent

A

Mobile elements : 45%, Repetitive sequences : 50%, Genes : 55%, Tandem repeats : 5%

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20
Q

What are TRs + what they do

A

Tandem repeats : consecutive repeats of DNA sequences that code for functional RNAs (and not proteins)

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21
Q

% of total human genome that is protein-coding regions

A

Approx 1.2%

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22
Q

Def. of simple sequence DNAs

A

direct repeats of 3-50 bases.

23
Q

Where simple sequence DNAs may be found (3)

A

Telomeres, centromeres, within genes

24
Q

How simple sequence DNAs are related to some human genetic diseases

A

Simple sequence is within a gene and expands -> becomes toxic (ONLY IF IN GENE)

25
Q

Ex. of disease due to simple sequences DNAs expanding in genes

A

Huntington disease : trinucleotide repeat of CAG expands

26
Q

How expansion simple sequence DNAs happens

A

splippage to form a loop during replication due to thermal energy -> one daughter DNA contains an extra repeat of the sequence

27
Q

How southern blot helps detecting number of repeats of a simple sequence DNA

A

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

28
Q

Why southern blotting of DNA fragments with simple sequence DNA gives diff. results from one person to another

A

Each person has a different number of the simple sequence DNA found at each site where it is present (polymorphism)

29
Q

MEDIRs distribution, length, number and genome %

A

Mobile element-derived interspersed repeats.

Interspersed, 100 - 10k bps, more than 1M copies, 45% of human genome

30
Q

MEDIRs what is the consequence of the fact that they can move

A

Can increase in number over evolutionary time

31
Q

MEDIRs their function for the organism + nickname

A

No function for the organism : ‘‘Selfish DNA’’

32
Q

what is a germ line

A

germ cells that come from earlier germ cells

33
Q

Frequency of germ line element transposition events

A

1 germ line transposition (out of the >1M MEDIRs) in one person in 8 (compared with their parents)

34
Q

2 major classes of MEDIRs and what differentiates them

A

1) DNA transposons
2) Retrotransposons
Different by their mechanism of transposition

35
Q

DNA transposons how transposition works

A

Direct transposition at DNA level.

36
Q

DNA transposons : what is the participating enzyme + where it comes from ?

A

Participating enzyme = transposase (ENCODED IN THE ELEMENT ITSELF)

37
Q

Retrotransposons how transposition works

A

Indirect transposition via an RNA intermediate

38
Q

Retrotransposition : what is the participating enzyme (2) + where it comes from ?

A

RNAP (cellular), Reverse transcriptase (encoded in the element itself)

39
Q

DNA transposons 2 steps mechanism

A

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)

40
Q

2 recognizable sites before and after MEDIRs transposition

A

Former transposon site and Insertion site

41
Q

3 steps mechanism of retrotransposons transposition

A

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

42
Q

Cut and paste transposition during DNA replication consequence/what MEDIR is concerned

A

increase of genomic copy number of DNA tranposons

43
Q

Cut and paste transposition 3 steps

A

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

44
Q

What viruses retrotransposons are related to

A

retroviruses like AIDS virus HIV

45
Q

(3) Major classes of retrotransposons in the human genome

A

LTR elements
LINEs
SINEs

46
Q

What LTR elements are

A

(retrotransposons) contain Long Terminal Repeats, like retroviruses

47
Q

What LINEs are + length + something particular they do

A

(retrotransposons) Long Interspersed Elements 1 to 6 kb

Code for proteins involved in their own retrotransposition

48
Q

What SINEs are + length + why considered parasites for LINEs

A

(retrotransposons) Short Interspersed, 300 bp, do not encode proteins but may use LINE-encoded proteins

49
Q

When accumulation of mobile elements is a problem and when it is not

A

Problem if happens within genes. If outside genes, makes no difference

50
Q

What happens to mobile elements over time (once copied/pasted)

A

Accumulate mutations and differ more and more of their parent molecule and their sibling molecule.

51
Q

What most of the non-repetitive non-coding DNA in the human genome is thought to be

A

Ancient mobile elements that undercame so many mutations that their ressemblance is not recognizable

52
Q

Important distinction between DNA transposons and retrotransposons IN TRANSPOSITION

A

DNA transposons : changes place (0 new copies)

Retrotransposons : Makes a copy that goes somewhere else (1 new copy)

53
Q

Important distinction between DNA transposons and retrotransposons IN THEIR INCREASE IN NUMBER

A

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

Biol 200 (30 decks)

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