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Hilary Term 1 > Organization of eukaryotic genomes > Flashcards

Organization of eukaryotic genomes Flashcards

1
Q

… orders of magnitude difference from smallest to the largest eukaryotic genome

A

5

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2
Q

Describe the genome of Encephalitozoon cuniculi

A

2.9 X 106 bp

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3
Q

Describe the genome of Homo sapiens

A

6 X 109 bp

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4
Q

Describe the genome of Paris japonica

A

1.5 X 1011 bp

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5
Q

Every human cell has … of DNA packaged into a sphere …

A

2m, 1 x 10-5m across

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6
Q

The combined length of DNA in a human is … the diameter of our solar system

A

4x

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7
Q

Every body has … cells

A

~ten trillion

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8
Q

Each one of us has
… km of DNA

A

~2 x 10^10

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9
Q

Describe the packaging of DNA

A
  • naked DNA is packaged into nucleosomes
  • into chromatin fibres
  • into topologically associated domains
  • into an individual chromosome
  • in the nucleus
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10
Q

DNA encodes every component needed to…

A

build, operate, maintain, and reproduce an organism.

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11
Q

What are the two main delineations of the eukaryotic genome?

A
  • transcribed into RNA
  • not transcribed
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12
Q

What are the two main delineations of transcribed DNA?

A
  • protein coding genes (1%)
  • non-coding genes (3%)
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13
Q

Describe the transcribed sequences that form protein coding genes

A

mRNA

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14
Q

Describe the transcribed sequences that form non-coding genes

A
  • tRNA
  • rRNA
  • snRNA
  • snoRNA
  • lncRNA
  • siRNA
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15
Q

Describe the major delineations of the non-transcribed DNA

A
  • structural
  • non-structural
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16
Q

Describe the structural elements of DNA

A
  • telomeres
  • centromeres
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17
Q

Describe the major delineations of the non-structural DNA

A
  • unique (35%)
  • repetitive (50%)
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18
Q

Describe the unique DNA

A
  • CNE
  • non-conserved non coding elements
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19
Q

CNE

A

conserved non-coding elements

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20
Q

Describe the repetitive DNA segments

A
  • satellite DNA
  • retrotransposons
  • LINEs
  • SINEs
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21
Q

Describe a protein coding RNA

A
  • 5’ Cap and UTR
  • CDS
  • 3’UTR
  • polyA tail
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22
Q

Describe protein coding DNA

A

exons separated by introns

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23
Q

Describe the relationship between gene number and bp length

A

Normally distributed

24
Q

The average CDS … bp

A

~1,000

25
Q

Longest CDS (Titin)

A

~90,000 bp

26
Q

The average gene … bp

A

~20,000

27
Q

Longest gene (dystrophin)

A
  • ~2.2 million bp
  • CDS = 14,000bp
  • 16hrs to transcribe
28
Q

Modal exon length

A

~ 111bp (37 codons)

29
Q

nucleosome

A

1 DNA packaging unit

30
Q

It takes …bp of DNA to wrap twice around a nucleosome + …bp spacer each side
(…bp total)

A

147, 33, 213

31
Q

of all exons shorter than 213bp

A

~90%

32
Q

Only … of human genes have only 1 exon

A

5%

33
Q

… of human genes have 2 or more exons

A

95%

34
Q

… exons is most common number

A

4

35
Q

Dystrophin has … exons

A

79

36
Q

Titin has … exons

A

363

37
Q

Describe the average human gene

A
  • 4 exons
  • 1000bp CDS
  • 20,000bp genomic footprint
  • 95% intron
38
Q

Protein coding genes are …

A

not uniformly distributed on chromosomes

39
Q

What is the function of the centromere?

A

attach chromosomes to spindle

40
Q

Describe the centromere

A
  • region of chromosome that links pair of sister chromatids
  • where spindle fibers attach via kinetochores in mitosis
  • usually one per chromosome
  • 5 million bp long in humans
  • mostly composed of α-satellites
  • 10% of the genome
41
Q

α-satellites

A

171bp repeats

42
Q

What is the function of the telomeres?

A

protect chromosome ends from degradation

43
Q

Describe the telomeres

A
  • at both ends of each chromosome
  • ~10,000 bp
  • thousands of repeats of “TTAGGG”
  • 3’ Single strand overhang which invades the double helix to form a T-loop
  • 1% of the genome
44
Q

Regions next to telomeres tend to have …

A

higher gene density

45
Q

Describe the relationship between telomeres and recombination

A

Sub-telomeric regions most frequently exchanged during recombination

46
Q

Describe “satellite” DNA

A
  • 1–6 bp simple tandem repeats
  • 3% of the genome
47
Q

What causes satellite DNA?

A

DNA replication errors

48
Q

What percentage of the genome is DNA replication errors?

A

3%

49
Q

Describe DNA replication errors

A
  • slippage and realignment
  • misalignment
50
Q

Describe the two possibilities of misalignment post-extension

A
  • +1 repeat mutation: 12-repeat allele after subsequent DNA replication
  • -1 repeat mutation: 10-repeat allele after subsequent DNA replication
51
Q

What is one method of DNA rescue?

A

DNA mismatch repair

52
Q

List some retrotransposons

A
  • LTRs
  • LINEs
  • SINEs
53
Q

Describe retrotransposon formation

A
  • formation of ribonuceloprotein complices undergo reverse transcription and integration
  • then transcribed and translated
54
Q

Describe retrotransposons

A
  • encode proteins that facilitate retrotransposition
  • kept inactive by RNAi
  • older ones mostly mutated and thus inactive
  • ~47% of your genome
55
Q

Describe LTRs

A

gag and pol type genes

56
Q

Describe LINEs and SINEs

A

encode reverse transcriptase and other proteins

57
Q

Describe the average human gene

A
  • 4 exons encoding an 1000 bp long mRNA
  • footprint of the gene is 20,000bp long
    ~30% of an average gene is LINEs, SINEs, and SSRs

Hilary Term 1 (61 decks)

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