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GENE 418: Human Genetics > Moderately repetitive fraction of the human genome > Flashcards

Moderately repetitive fraction of the human genome Flashcards

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1
Q

What is the major contributor to this fraction?

A

Multigene families

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2
Q

Are gene families common in protein coding genes?

A

Very. 50-75% of protein coding genes belong to a family

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3
Q

What is included in a gene family?

A

Protein coding genes, pseudogenes, and gene fragments with sequence similarity

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4
Q

What are the 3 types of gene families?

A

Classical, domain-based, motif based

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5
Q

What is a classical gene family?

A

A gene family whose members show a high degree of sequence homology over most of the gene length, especially in the coding region

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6
Q

Are genes that are part of the same family clustered in the same area or dispersed through the genome?

A

Can be either

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7
Q

What type of gene family are the globin and Pax gene families?

A

Classical

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8
Q

What is a domain based gene family?

A

A gene family whose members have a high degree of sequence similarity within a protein domain

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9
Q

How similar will the gene sequences between members of a domain-based family be?

A

Highly similar within the domain, but much lower everywhere else

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10
Q

What type of gene family are the Hox genes?

A

Domain-based

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11
Q

What is a motif-based gene family?

A

A gene family whose members have a high degree of sequence similarity within a specific protein motif of conserved AA with a specific function

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12
Q

How similar will the gene sequences between members of a motif-based family be?

A

High homology over the motif, but not much else

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13
Q

What type of gene family do RNA helicases with a DEAD box belong to?

A

Motif-based

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14
Q

What is a pseudogene?

A

Defective copies of genes with much of the sequence intact, but with a pile of accumulated mutations that result in it having no function

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15
Q

What are gene fragments?

A

A smaller duplicated region of a gene, like a single exon

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16
Q

What are the two types of pseudogenes?

A

Processed and unprocessed/classical

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17
Q

How do processed pseudogenes happen?

A

Reverse transcription of a processed mRNA that then got inserted into the genome

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18
Q

What do processed pseudogenes look like?

A

Only exons, no introns or regulatory sequences. Might find a polyA tail

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19
Q

Are processed pseudogenes expressed?

A

Not usually

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20
Q

Where will processed pseudogenes typically integrate?

A

Right in the middle of the genome far away from any regulatory sequences. Most of the time won’t be expressed and will accumulate mutations into retropseudogenes

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21
Q

Where could processed pseudogenes rarely integrate?

A

Next to some promoters and regulatory elements with the right spacing. These might be expressed, and they would be retrogenes

22
Q

If a pseudogene gets expressed, will it encode a protein?

A

Sometimes, but can also just be expressed as a transcript

23
Q

How do unprocessed pseudogenes happen?

A

Gene duplication events

24
Q

What do unprocessed pseudogenes look like?

A

Exons and introns and some flanking sequences

25
Q

Are unprocessed pseudogenes expressed?

A

Sometimes. But they’ve accumulated so many mutations that they usually aren’t functional

26
Q

What are two classifications of transposable elements?

A

TEs that move via an RNA intermediate (copy and paste) or via a DNA intermediate (cut and paste)

27
Q

How can transposable elements that move via an RNA intermediate be classified further?

A

Whether they can encode their own reverse transcriptase or not

28
Q

What type of transposable elements that move through an RNA intermediate can’t encode their own reverse transcriptase?

A

Non-viral family TEs like Alu sequences

29
Q

How can transposable elements that move via an RNA intermediate AND encode their own reverse transcriptase be classified further?

A

Whether they have long terminal repeats (LTR) or not

30
Q

What type of transposable element moves through an RNA intermediate, encodes its own reverse transcriptase, and has long terminal repeats?

A

Retroviral-like transposons

31
Q

What type of transposable element moves through an RNA intermediate, encodes its own reverse transcriptase, and doesn’t have long terminal repeats?

A

LINE elements

32
Q

What are LINE elements?

A

Long interspaced nuclear elements

33
Q

Are LINE elements autonomous?

A

Yes, they encode their own reverse transcriptase

34
Q

What do the two ORFs in a full size LINE element encode?

A
  1. p40 - protein with unknown function

2. Reverse transcriptase/endonuclease

35
Q

How large is a full size LINE element? What is part of it?

A

6.1 kb. Includes the two ORFs, an internal promoter, a polyA tail, and 7-20 bp direct repeats on each end

36
Q

Where are LINE elements usually found in the human genome?

A

G-bands - A/T rich regions with few genes

37
Q

What are Alu elements?

A

A type of SINE (short interspersed nuclear repeat) that arose from 7SL RNA

38
Q

What do Alu elements look like?

A

100-400 bp, internal promoter but no ORFs, flanked by 6-18 bp direct repeats

39
Q

Are LINEs common in humans?

A

Very, about 850 000 of them in humans. 21% of our genome

40
Q

Are Alu elements common in humans?

A

Very, ~1.5 million of them. Make up about 13% of our genome

41
Q

What do LTR retrotransposons strongly resemble?

A

Retroviruses

42
Q

What are the 4 basic structural elements of a retrovirus genome?

A
  1. gag - encodes RNA binding proteins/virus core
  2. pol - encodes reverse transcriptase and processing enzymes
  3. env - outer coat proteins
  4. flanking long terminal repeat sequences
43
Q

What genomic element of retroviruses are LTR retrotransposons missing?

A

env - doesn’t encode any viral coat proteins

44
Q

How much of our genome is made up by LTR retrotransposons?

A

8%

45
Q

What are DNA transposons?

A

Transposable elements that move through cut and paste DNA intermediates

46
Q

What do DNA transposons look like?

A

ORF encoding transposase, flanked by short inverted repeats

47
Q

How much of our genome is made up of DNA transpososns?

A

3%, there’s about 300 000 of them

48
Q

Are Alu elements evenly distributed across the genome?

A

No, are more likely to be found in R-bands with a higher G/C content

49
Q

Are LTR retrotransposons evenly distributed across the genome?

A

Pretty consistent across G/C content

50
Q

Are DNA transposons evenly distributed across the genome?

A

Pretty consistent

GENE 418: Human Genetics (31 decks)

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