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Alex's Genetics > Lecture 16b > Flashcards

Lecture 16b Flashcards

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Biology 101 flashcards
1
Q

Describe 3 aspects of unique or non-repetitive sequences.

A

-Found in two copies (one from mom and one from dad)
-Includes structural genes as well as intergenic areas
-In humans, make up roughly 40% of the genome

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2
Q

Describe 2 aspects of moderately repetitive DNA sequences.

A

-Found a few hundred to a few thousand times
-Includes genes for rRNA and histones

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3
Q

Describe 3 aspects of highly repetitive DNA sequences.

A

-Found tens of thousands to millions of times
-Each copy is relatively short (a few nucleotides to a few thousand in length)
-Some of these sequences are clustered together in tandem arrays

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4
Q

Name 3 examples of moderatively repetitive DNA sequences.

A

-Genes for rRNA and histones
-Origins of replication
-Some transposable elements

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5
Q

Name 3 examples of highly repetitive DNA sequences.

A

-Alu transposable elements in humans (11% of human DNA)
-LINE-1 transposable elements in humans (20% of human DNA)
-ERV elements (Endogenous Retroviruses)(8% of human DNA)

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6
Q

What are the two types of retrotransposons?

A

LTR and Non-LTR transposons

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7
Q

Describe LTR retrotranspositions.

A

These are long terminal repeats which are typically a few hundred nucleotides long. They are evolutionarily related to known retroviruses.

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8
Q

What do LTR retrotransposons do?

A

Like their viral counterparts, they encode viral related proteins that are needed for the transposition process.

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9
Q

How are LTR retrotransposons categorized?

A

Based on their evolutionary relationship to retroviral sequences.

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10
Q

What are retroviruses?

A

RNA viruses that make a DNA copy that integrates into the host’s genome.

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11
Q

Do humans have LTR transposons? If not, what do humans have?

A

Humans do not have genuine LTR transposons but they do have endogenous retroviruses (ERVs) that resemble LTR transposons.

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12
Q

Name 3 examples of things that have LTR transposons.

A

-Budding yeast and other fungi
-Fruit flies
-Plants

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13
Q

In plants, _______ ____________________ tend to be the _________ class of _______________ sequences.

A

In plants, LTR retrotransposons tend to be the largest class of repetitive sequences.

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14
Q

What does the integrase protein do in regards to a non-LTR retrotransposon?

A

Some retrotransposons have an integrase gene, which produces an integrase protein that will insert a DNA copy of a non-LTR retrotransposon into chromosomal DNA.

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15
Q

T/F: Alu and LINE-1 are LTR retrotransposons.

A

False! Alu and LINE-1 are non-LTR retrotransposons.

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16
Q

What does LINE-1 stand for?

A

Long interspersed nuclear elements

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17
Q

How long is LINE-1 and how common is it?

A

LINE-1 is up to 6-kb long. It is found in around 900,000 copies per genome.

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18
Q

What does SINEs stand for?

A

Short interspersed nuclear elements

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19
Q

How long are SINEs?

A

Less than 500-bp in length

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20
Q

What is an example of SINEs and how common are they?

A

Alu sequence is an example.

Present in over 1,000,000 copies in the human genome.

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21
Q

T/F: The ___ family of retroelements does not share any __________ similarity with viruses.

A

The Alu family of retroelements does not share any sequence similarity with viruses.

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22
Q

Where is the Alu family of retroelements derived from?

A

It is derived from a single ancestral known as the 7SL RNA gene that is part of a RNA-protein complex.

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23
Q

What does the RNA-protein complex (that the 7SL RNA gene is part of) do?

A

It transports proteins carrying a specific sequence (signal) to the endoplasmic reticulum (while they are still being synthesized).

24
Q

How many copies in humans has the Alu gene sequence been copied by retrotransposition into?

A

Greater than 1,000,000 copies in humans.

25
Q

T/F: Alu elements encode for several proteins.

A

False! Alu elements do NOT encode for any proteins

26
Q

How are Alu elements replicated?

A

They hijack proteins made by LINE elements and is then replicated.

27
Q

Generally speaking, what does the 7SL RNA do?

A

It helps with the secretion of proteins.

28
Q

If proteins are to be secreted, what first needs to happen?

A

To be secreted, they need to first be targeted to the plasma membrane in bacteria and archaea or to the ER membrane in eukaryotes.

29
Q

What brings proteins to the ER membrane in eukaryotes?

A

The signal recognition particle (SRP), an RNA-protein complex, facilitates this targeting process.

30
Q

____ transposons are derived from the ____ component of the _____.

A

Alu transposons are derived from the RNA component of the SRP.

31
Q

T/F: The mechanism for retrotransposition of a non-LTR retrotransposon is very well understood.

A

False! This mechanism is not fully understood.

32
Q

Describe the process of retrotransposition of a non-LTR retrotransposon.

A

1) A non-LTR retrotransposon is transcribed into an RNA.
2) A site on the target DNA is cleaved and the retrotransposon RNA polyA binds to the site.
3) Reverse transcriptase copies the RNA into DNA and the target DNA is cleaved at a second site.
4) The RNA is degraded and only the retrotransposon is put into the target site. DNA is filled in by DNA polymerase and ligase.

33
Q

When are transposons autonomous?

A

When they contain all the information necessary for transposition to occur.

34
Q

When are transposons non-autonomous? What is an example of this?

A

When they lack a gene that is necessary for transposition/mobilization to occur.

Alu elements are non-autonomous.

35
Q

What is the Selfish DNA Theory?

A

This was the original interpretation of retroelements.

Basically, it says that retroelements behave like intracellular parasites. They can proliferate in the host as long as they do not harm the host to the extent that they significantly disrupt survival.

36
Q

Transposable elements can _________ enter the ________ of an organism and _____________ quickly.

A

Transposable elements can rapidly enter the genome of an organism and proliferate quickly.

37
Q

Describe the event with Drosophila melanogaster (fruit flies) and P element.

A

A transposable element known as the P element was introduced into fruit flies in the 1950s. In the last 50 years, the P element has expanded throughout the fruit fly population worldwide.

38
Q

Where are the only strains of fruit flies without the P elements located?

A

In lab stocks collected prior to 1950.

39
Q

What is the more recent view on retroelements?

A

That they exist because they offer an evolutionary advantage.

40
Q

Bacterial retroelements carry ___________-resistance genes, which may cause greater ___________ ____________ through recombination.

A

Bacterial retroelements carry antibiotic-resistance genes, which may cause greater genetic variability through recombination.

41
Q

What can retroelements cause?

A

The insertion of exons into the coding sequences of structural genes (aka exon shuffling).

42
Q

______ _________ has led to the evolution of genes with more diverse functions.

A

Exon shuffling

43
Q

What is exon shuffling?

A

The transfer of exon(s) from one gene into another gene by homologous recombination between repeats / within introns.

44
Q

T/F: Transposable elements do not affect chromosome structure and gene expression.

A

False! Transposable elements have a variety of effects on chromosome structure and gene expression.

45
Q

What is an example of an effect that a transposable element can have on gene expression?

A

Heterochromatin can spread from a transposable element and silence a nearby gene.

46
Q

T/F: Heterochromatin is always stable.

A

False! Heterochromatin can be unstable.

47
Q

What are 2 ways in which heterochromatin can be unstable?

A

1) Heterochromatin can spread and contract influencing nearby genes differently in different people.
2) If a transposable element loses its heterochromatin, this can expose DNA sequences that may alter the expression of nearby genes.

48
Q

T/F: Transposons always act as silencers.

A

False! Some transposons have DNA sequences that function as enhancers or promoters.

49
Q

What is the regulation of transposition and why?

A

It is highly regulated because many outcomes can be harmful.

50
Q

What stimulates transposition/the movement of transposable elements?

A

Stress agents such as radiation, chemical mutagens, and hormones.

51
Q

What is epigenetic gene inheritance?

A

Heritable gene expression or gene silencing that can be passed down from cell to cell or generation to generation.

52
Q

Is epigenetic gene inheritance reversible? Does it involve changes in the DNA sequence?

A

It is reversible.

It does NOT involve a change in the DNA sequence.

53
Q

What is an example of epigenetic gene regulation?

A

The heterochromatin at the Beta-globin locus.

54
Q

Describe Constitutive Heterochromatin.

A

It forms over repetitive sequences and spreads beyond the repetitive sequences.

55
Q

What forms continuous heterochromatin domains? What effect do these have?

A

Clusters of repetitive sequences. These can then silence nearby genes.

56
Q

What predominates wherever there are lots of repetitive sequences?

A

Heterochromatin. This is in places such as centromeres and telomeres.

Alex's Genetics (38 decks)

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