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Molecular Biology- Emily > Eukaryotic Genome Structure > Flashcards

Eukaryotic Genome Structure Flashcards

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1
Q

How are comparisons of genome size made?

A

At the haploid level.

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2
Q

Give reasons why genome size doesn’t necessarily correspond to complexity.

A

Humans have a smaller haploid genome than some species. There are large differences in genome size between organisms with the same body plan and metabolism.

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3
Q

What is the C-value in the C-value paradox?

A

The amount of DNA in the haploid genome.

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4
Q

Give evidence that more non-coding DNA results in more complexity.

A

Susumu Ohno showed that there were a limited number of functional gene loci, and after this there would be too much coding DNA, which would be detrimental to the organism.
Puffer fish has a high amount of non-coding DNA that it doesn’t not require, but does not remove as this would require a high amount of energy.

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5
Q

How can an increase in complexity be explained when there is more non-coding DNA?

A

Eukaryotes have sophisticated gene regulation systems, approx. 9% of genes code for transcription factors.
Splicing and alternative splicing also increase complexity.

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6
Q

How is the complexity of DNA defined?

A

The number of unique sequences present in a genome.

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7
Q

What is Cot analysis?

A

Identifies types of unique/repetitive DNA, by denaturing dsDNA and following the speed of renaturation.

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8
Q

How is Cot analysis carried out experimentally?

A
  1. Mechanically shear DNA to 400bp.
  2. Denature the DNA at 100°C.
  3. Slowly cool to allow renaturation. Measure the % of ssDNA at specified time points.
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9
Q

What are the 3 types of DNA found in a eukaryotic genome?

A

Highly repetitive, Moderately repetitive and single/low copy.

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10
Q

What type of sequences renature first?

A

Highly repetitive DNA.

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11
Q

Where in a chromosome is there a low frequency of genes?

A

At the centromere.

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12
Q

What are pseudogenes?

A

Genes where mutations have occurred that knock out the gene function.

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13
Q

What are retrogenes?

A

Reactivated pseudogenes.

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14
Q

What are multigene families?

A

Groups of identical or similar sequences, that can be tandemly arranged differently in different organisms.

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15
Q

What is a complex gene family? Give an example.

A

Genes that have diverged from each other despite being tandemly arranged, e.g. the β globin gene.

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16
Q

What is a dispersed gene family? Give an example.

A

Genes that have not been tandemly arranged but have become dispersed at several locations in the genome as a result of chromosomal rearrangements, e.g. the aldolase gene family with genes located on 5 chromosomes.

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17
Q

What is spacer DNA?

A

Intergenic DNA with non-sequence specific functions.

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18
Q

What are the roles of spacer DNA?

A
  • Allows for the flexibility of the 3D structure of DNA.
  • Allows for transcription factor binding sites.
  • Allows for complex regulatory mechanisms.
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19
Q

What is the contour length of DNA?

A

The length of DNA in a genome that is assuming a B-form double helix.

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20
Q

How is the barrel shaped core histone octamer made?

A
  1. Two H3/H4 dimers form.
  2. These form a tetramer.
  3. Two H2A/H2B dimers form and bind to the tetramer.
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21
Q

What is the Nucleosome Core Particle (NCP)?

A

A histone octamer with DNA wrapped around it.

22
Q

How many base pairs of DNA interact with a histone octamer?

A

146 bp.

23
Q

How do histones interact with DNA?

A

Histones are cationic (lots of Lys/Arg) so bind to the negatively charged DNA backbone. Histones select the regions of DNA that are easiest to bend. Histones bind to the minor groove of DNA.

24
Q

What is the chromatosome?

A

A nucleosome with the H1 linker histone bound, fixing the octamer to the DNA.

25
Q

Why does nucleosome distribution vary between chromosomal loci?

A

Nucleosome binding is sequence dependent. Histone octamers can migrate to allow transcription.

26
Q

What is a DNA solenoid?

A

Chromatin that has been condensed by zig-zag folding into a 30nm fibre.

27
Q

How is the solenoid stabilised?

A

By H1 binding.

28
Q

How much are sequential NCPs rotated in a solenoid?

A

By 71°.

29
Q

What does the extent of solenoid compaction depend on?

A

Depends on the cellular environment. If transcription is needed the solenoid opens up.

30
Q

How many nucleosomes are there per helical turn in a solenoid?

A

6.

31
Q

What did experiments with lamp-brush chromosomes show?

A

Solenoids are organised as looped domains in a radial arrangement, along scaffold proteins (H1/Sc1/Sc2).

32
Q

What regions of DNA do scaffold proteins bind to?

A

AT-Rich regions.

33
Q

How is the DNA scaffold further condensed?

A

By generating supercoils.

34
Q

What does a chromosome consist of?

A

Helically packed loops of 30nm fibres.

35
Q

What is euchromatin?

A

Condensed chromatin that is transcriptionally active. Contains the largest proportion of genes in a chromosome.

36
Q

What is heterochromatin?

A

Condensed chromatin that is less transcriptionally active than euchromatin.

37
Q

What is faculative chromatin?

A

Chromatin that can be changed from heterochromatin to euchromatin.

38
Q

What is constitutive chromatin?

A

Chromatin that is condensed as heterochromatin throughout the cell cycle.

39
Q

What are telomeres?

A

Protective terminal regions of a chromosome that get shorter as organisms get older.

40
Q

What do telomeres consist of?

A

A repeated sequence.

41
Q

Why are telomeres needed?

A

To distinguish between real chromosome ends and double stranded breaks within a chromosome that needs fixing.

42
Q

How can a gene be defined as a complementation unit?

A

Genes are a series of mutant alleles that fall into a single complementation group.

43
Q

How can a gene be defined as a transcription unit?

A

Genes are lengths of DNA which are transcribed into mRNA.

44
Q

What is complementation?

A

Different mutations are partly or entirely cancelled out when they occur together, giving a functional genome.

45
Q

What are complementation tests used for?

A

To see if recessive mutations that result in the same phenotype are on the same gene or on different genes.

46
Q

How are complementation tests carried out?

A

Cross the homozygous mutant for mutation A with the homozygous mutant for mutation B. If mutations are on different genes, they will complement each other and the progeny shows the normal phenotype. If mutations are on the same gene, they affect the same functions and cannot complement each other- the progeny shows the mutant phenotype.

47
Q

What type of genes are unsuitable for complementation testing?

A

Genes that have been alternatively spliced.

48
Q

How was the colinearity of the genetic map and the amino acid sequence shown by Yanofsky?

A

Isolated trpA mutants and defined the altered amino acid sequence for each mutant protein. This showed that the further apart mutations were, the further apart the altered amino acids were.

49
Q

What are hotspots?

A

Regions of the genome that are more prone to mutation.

50
Q

What evidence suggests that mutations are random and not at hotspots?

A

Mutations are not uniformly distributed in the genome. Mutations can only be recovered if the function is also recovered. Therefore mutations at cold spots must still occur but not affect function (are silent).

Molecular Biology- Emily (7 decks)

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