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Genetics, Cancer and Development Emily > 001 Structure of the human genome > Flashcards

001 Structure of the human genome Flashcards

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1
Q

describe the 6 layers of genome organisation from DNA strands

A
  1. DNA double helix
  2. DNA double helix strands wrapped around histone proteins to form nucleosome
  3. nucleosomes packed together in a fiber to form chromatin
  4. lots of chomatin strands together form chromosome
  5. chromosome is condensed
  6. 2 sister chromatids join at the centromere to form a chromosome
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2
Q

what is a nucleosome?

A

DNA wrapped around histone proteins

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3
Q

what is a chromatin?

A

lots of nucleosomes (DNA wrapped around histone proteins) packed together to form chromatin

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4
Q

what is a chromatosome?

A
  • nucleosome and 1 histone protein
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5
Q

what is a chromosome

A

packaged DNA wrapped around histone proteins carrying genetic information
- 2 sister chromatids form a chromosome

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6
Q

what is a chromatid?

A
  • one of the 2 identical halves of a chromosome that has been replicated for cell division
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7
Q

what is the human genome split into?

A
  • nuclear genome
  • mitochondrial genome
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8
Q

what is the nuclear genome split into?

A
  • genes and gene-related sequences (30%)
  • extragenic DNA (70%)
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9
Q

what is genes and gene-related sequences split into?

A
  • coding DNA
  • non-coding DNA
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10
Q

what is non-coding DNA split into?

A
  • pseudo-genes (resembles a gene but does not code for anything)
  • introns, leaders, trailers, promoter regions (parts of a gene that influence expression of gene)
  • gene fragments
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11
Q

what is extragenic DNA and what is it split into?

A
  • DNA between genes
  • split into repetitive DNA and unique/low copy number
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12
Q

what is repetitive DNA split into?

A
  • tandemly repeated DNA
  • interspersed genome-wide repeats
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13
Q

what are the 3 types of tandemly repeated DNA?

A
  • satellite
  • minisatellite
  • microsatellite
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14
Q

what are the 4 types of interspersed genome-wide repeats?

A
  • LTR elements (long terminal repeats)
  • LINEs (long interspersed retrotransposable elements)
  • SINEs ( short interspersed retrotransposable elements) - DNA transposons
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15
Q

what are DNA transposons?

A

= move from one genomic location to another by a cut-and-paste, can be used to introduce a piece of foreign DNA into a genome

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16
Q

what are the 6 components to a typical gene?

A
  • exons (coding part)
  • introns (non-coding part)
  • 5’UTR (untranslated region) directly upstream of initiation codon
  • 3’UTR (untranslated region) directly after termination codon
  • promoter region/ TATA box/ transcription factors upstream to gene where RNA polymerase binds and begin/regulatates transcription
  • upstream enhancers/silencers
17
Q

how is DNA altered to produce mature mRNA?

A
  • add 5-methyl guanosine cap and 3’ poly-A tail
  • remove introns (splicing)
18
Q

what are exons?

A
  • coding part of DNA and mature mRNA
  • codes for proteins
19
Q

what are introns?

A
  • non-coding part of coding region of DNA
  • removed via splicing to form mature mRNA
20
Q

generally in DNA, are there more introns or exons?

A
  • more introns than exons
21
Q

whats the relationship between proportion of introns and size of gene?

A
  • the larger the gene, this bigger the proportion of introns
  • the larger the gene the smaller the proportion of exons
22
Q

what are genes within genes?

A

you can get small genes within introns of larger genes

23
Q

describe the relationship between gene densities and size of region

A
  • the larger the number of bases, the lower the gene density
24
Q

what are some different features of gene families?

A
  • members may exhibit high sequence homology (similarity of bases conserved through evolution)
  • sometimes contain a highly conserved domain
  • sometimes contain a very short conserved motif sequence
  • superfamilies (e.g. immunoglobulin superfamily)
  • sometimes clustered (globin genes)
  • often associated with truncated (lost function) and non processed pseudo genes (e.g. salivary amylase)
25
Q

describe the length and location of satellite DNA

A
  • 100kb to 5Mb
  • repeat = 5bp-5kb
  • locations = heterochromatin (regions of genome that are gene poor and very variable), particularly at centromeres
26
Q

describe the length and location of minisatellite DNA

A
  • 0.1-20kb
  • repeats = 6-64bp
  • scattered but concentrated near telomeres
27
Q

describe the length and location of microsatellite DNA

A
  • <100 bp
  • repeats = 1-5bp
  • dispersed throughout genome
28
Q

describe a use of satellite DNA

A
  • used in forensics/DNA fingerprinting as the number of repeats are very variable as there is a very high chance the number of repeats will change from parent to offspring
  • making them almost completely unique in each individual
29
Q

describe ultracentrifugation of satellite DNA

A
  • DNA has a density of 1.8g/ml
  • Filling DNA with a CsCl solution (high density) and then centrifuging the solution causes DNA to float and form bands at different densities
  • satellite bands form above the main DNA band as they are shorter so less dense
30
Q

give some examples of dispersed repetitive DNA

A
  • SINE, LINE ( short and long interspersed retrotransposable elements)
  • LTR elements (Long terminal repeats)
  • DNA transposons
  • Alu = a family of SINE repeats ( very common in genome)
31
Q

why do mitochondria have their own DNA?

A
  • use for oxidative phosphorylation to produce ATP (need to live)
  • endosymbiotic theory = mitochondria used to be free living prokaryotes, and thus needed their own DNA
32
Q

describe the structure/differences of mitochondrial DNA

A
  • it is naked ( not associated with histone proteins)
  • circular (continuous ring, similar to prokaryotes)
  • very gene-rich with little ‘junk DNA’
  • has 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes
33
Q

what is the mutation rate of mitochondrial DNA vs nuclear DNA?

A

much higher mutation rate of mitochondrial DNA than nuclear DNA as mitochondrial DNA produces a lot more free radicals

34
Q

how does the size of mitochondrial DNA compare to nuclear DNA?

A
  • mitochondrial DNA is much smaller
  • 1/180,000 the size of nuclear genome
35
Q

how does mitochondrial DNA coding compare to nuclear DNA coding?

A
  • the same codons do not often code for the same thing, e.g. AGA codes for arginine in nuclear DNA and stop in mitochondria
  • not really a universal genetic code as such
36
Q

what is the pattern of mitochondrial inheritance?

A

mitochondria are in both males and females
- however the sperm does not contribute its mitochondria to the fertilised egg, only the egg mitochondria does
- therefore we only inherit mother’s mitochondrial DNA

Genetics, Cancer and Development Emily (8 decks)

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