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Human Molecular B > Lecture 1 - Organisation Of Human Gene > Flashcards

Lecture 1 - Organisation Of Human Gene Flashcards

1
Q

The genome

A

The complete DNA sequence of an organism to

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2
Q

C value

A

Refers to the amount of DNA contained within a haploid nucleus

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3
Q

What is C value measured in?

A

Pictograms or Kilobases

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4
Q

The number of genes in bacterial and archaea genome … with the genome size and the complexity of the organism

A

Correlates

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5
Q

The number of genes in a eukaryotes … with the genome size or the complexity of the organism

A

Does not correlate

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6
Q

How many genes in eukaryotes?

A

6000 to 40,000

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7
Q

DNA content of the haploid genome … with morphological complexity of lower eukaryotes but … among higher eukaryotes?

A

Increases Varies

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8
Q

What is the C value paradox?

A

The lack of relationship between DNA content (C Valerie) of an organism and it’s coding potential

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9
Q

What is the gene density of yeast?

A

496

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10
Q

What is the introns per gene for yeast ?

A

0.04

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11
Q

What is the gene density of fruit fly?

A

76

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12
Q

What is the introns per gene?

A

3

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13
Q

Genes occupy how much of the genome?

A

25%

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14
Q

The human genome has how many genes?

A

20,000 to 25,000

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15
Q

How much of the human genome consist of exons (protein coding sequences)?

A

1.2%

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16
Q

How much of the human genome consist of introns?

A

24%

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17
Q

How much of the genome is protein-binding sequence (I.s. Functional DNA elements)?

A

8.5%

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18
Q

In total how much of the human genome is functional ?

A

80%

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19
Q

What is DNA melting?

A

On heating DNA the two entwined complementary strands will completely separate into single strands. Melting involves progressive breaking of base pairs in the double helix

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20
Q

What is DNA melting determined by?

A

Base composition of DNA A:T base pairs melt at lower temperatures than G:C base pairs (2 vs 3 hydrogen bonds)

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21
Q

What is the Melting temperature (Tm)?

A

The temperature at which DNA is half unfolded (the double strands are 50% dissociated into single strands)

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22
Q

The higher the G:C ratio the …the Tm

A

Higher

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23
Q

What is the equipment used to create a DNA melting curve ?

A

Spectrophotometer

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24
Q

What is change in absorbance measured on a spectrophotometer?

A

260nm

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25
Q

Nucleotide bases absorb UV light at ymax of what?

A

260nm

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26
Q

What is hypochromicity?

A

Nucleotide vase pairs are neatly stacked and orientated in the DNA helix. They are “masked” and absorb less UV than unstacked randomly orientated based in single-stranded DNA

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27
Q

What is DNA reannealing also known as?

A

Renaturation

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28
Q

If melted DNA is … cooled complementary strands remain separated

A

Rapidly

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29
Q

If melting DNA is … cooled then complementary strands will pair up again

A

Slowly

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30
Q

What type of strands can reanneal?

A

Complementary

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31
Q

DNA reannealing is a basis of what?

A

DNA hybridisation

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32
Q

Mismatching in reannealing results in what?

A

Less stable DNA

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33
Q

What is the DNA reannealing measured in?

A

Cot value

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34
Q

How is cot calculated?

A

Concentration x time

35
Q

What is the cot measured in?

A

Mol sec -1

36
Q

What are the determinants of rage of Reannealig?

A

DNA concentration DNA fragment length DNA sequence composition and complexity

37
Q

What is the determinant of extent of reannealing?

38
Q

What is the complexity of poly A/U

39
Q

What is the complexity of E.coli DNA?

A

4.6 x10^6 bp

40
Q

What is Cot 1/2?

A

The Cot at which half the DNA has reannealed

41
Q

What is Cot 1/ proportional to of the DNA?

A

Complexity

42
Q

What do DNA reannealing experiments show for prokaryotes?

A

Prokaryotic genomes are kinetically simple

43
Q

Prokaryotic DNA reanneals as if it were ?

A

Single unique lengths

44
Q

What do DNA reannealing experiments show about eukaryotic genome?

A

Eukaryotic genomes are kinetically complex

45
Q

Eukaryotic genomes contain how many classes of DNA?

46
Q

What is the fast component?

A

Highly repeated DNA sequences

47
Q

What is the intermediate component?

A

Moderately repeated DNA sequences

48
Q

What is the slow component?

A

Non-repetitive or single-copy DNA sequences

49
Q

Why do components have different speeds?

A

Concentration of any single short sequence is reduced as the number of the different short sequences making up the whole mixture is increased. Therefore each sequence takes longer to find its complementary stand

50
Q

How much of the genome is composed of short sequences repeated many thousands of time?

A

Around 30%

51
Q

How much of the genome is composed of unique DNA or present in only a few copies?

A

Around 45%

52
Q

Repeated sequences (present n more than one copy) account for how much of the human genome?

53
Q

Where is highly repetitive DNA is present?

A

Almost all higher eukaryotic organisms. The amount varies from organism to organism

54
Q

Highly repetitive DNA make up how much of total chromosomal DNA in humans?

A

Around 25%

55
Q

Highly repetitive DNA make up how much of total chromosomal DNA in arthropods?

56
Q

What is the cot range of highly repetitive DNA?

A

Low cot range: 10-4 to 10-2

57
Q

What is the average copy number of highly repetitive DNA?

58
Q

What is the repeat length of highly repetitive DNA?

A

Few bases to several hundred

59
Q

Highly repetitive structural DNA

A

Virtually no coding function

60
Q

Repeat length of highly repetitive DNA?

A

Wide variety of repeats exist with a repeat unit varying from 2bp to 200bp

61
Q

What is the usual repeat length highly repetitive DNA?

62
Q

How are repeat units arranged?

A

Head to tail tandem array (blocks) of various length Interspersed in the chromosome

63
Q

What is the longest tandem array known in humans?

A

Alphoid DNA

64
Q

What is the total array length of alphoid DNA?

65
Q

How can tandemly repeated DNA be characterised?

A

Size (total array length not size of repeat unit) Satellite Mini satellite
Micro satellite

66
Q

Explain gradient centrifugation

A

Main band - most, random sequence DNA has a similar buoyant density Lighter band - if one short sequence is repeated many thousands of times in a tandem array, all the fragments of DNA derived fr this repeat have the same base composition and hence the same buoyant density. This is known as the satellite band containing satellite DNA

67
Q

What is the expansion of tandemly repeated human DNA caused by?

A

Unequal crossing over Replication slippage

68
Q

What is unequal crossing over?

A

Error in pairing and crossing-over I’m which non equivalent sites are involved in a recombination event. It produces one recombinant with a deletion of material and one with duplication

69
Q

What is Replication slippage?

A

Occurs when the daughter strand slips back one repeating unit in pairing with the template strand Each slippage event adds one repeating unit to the daughter strand

70
Q

Where are the chromosomal locations of satellite DNA?

A

Widely dispersed over the chromosome - microsatellite Telomere: tandem repeats of TTAGGG mini satellite. Length several Kb Preferentially in regions close to the telomere: hypervariable mini-satellite DNA Centromere: various satellite components. Length several Mb

71
Q

Intermediate repetitive DNA makes up how much of the total chromosome?

A

Around 30%

72
Q

What is the cot range for intermediate repetitive DNA?

73
Q

What is the average cost for number of intermediate repetitive DNA?

A

10^2 - 10^5

74
Q

What are the 3 classes for intermediate repetitive structural DNA?

A

Retrovirus/LTR retrotransposons LINES SINES

75
Q

What is LINES?

A

6.1kb LINe1 element has 2 open reading frame: 1-kB: ORF1 encodes an RNA-binding protein 4-KB: specifies a protein with both endonuclease and reverse transcriptase activities RNA-mediated transposition event An internal promoter lies within a region of untranslated DNA preceding ORF1 (5’UTR) Other end: (A)n/(T)n sequence ( 3’ poly (A) tail)

76
Q

What is the Retrovirus/LTR retrotransposon?

A

Encode for integrase and reverse transcriptase activities RNA-mediated transposition event

77
Q

What is SINES?

A

Alu repeat Consensus standard Alu diner is shown with 2 similar repeats terminating in an (A)n/(T)n like sequence Different sizes: insertion of a 32-no element within larger repeat Possess high sequence identity to 7S RNA About 300bp long Repeated about 106 times Alu DNA possess 85% sequence homology (related but not identical DNAs)

78
Q

What does intermediate repetitive DNA code for?

A

Genes for rRNA: situated in the nucleolus Genes for tRNA Protein coding genes eg. Histones, heat shock proteins and ubiquitins, collagen, keratin, actin myosin and tropomyosin, immunoglobulins, protein kinase transcription factor Transplantation antigens, ribosomal proteins

79
Q

Slow reannealing DNA make up how much of the chromosomal DNA in humans?

A

Around 45%

80
Q

Cot of slow reannealing DNA

A

High Cot value > 10^2

81
Q

What is the average copy number of slow reannealing DNA?

82
Q

Repeat length of slow reannealing DNA

83
Q

What is a special feature of slow reannealing DNA?

A

Unique Protein coding DNA: mRNA Non-Protein coding intergenic and intronic DNA (including ncRNA) Regulatory sequences

84
Q

What is the genome comprised of?

A

44% - interspersed repeated DNA 24% - introns 15% - unique non coding DNA 15% - Tandomly repeated DNA 10% - Alu elements 1.5% - exons

Human Molecular B (13 decks)

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