001 Structure of the human genome Flashcards
describe the 6 layers of genome organisation from DNA strands
- DNA double helix
- DNA double helix strands wrapped around histone proteins to form nucleosome
- nucleosomes packed together in a fiber to form chromatin
- lots of chomatin strands together form chromosome
- chromosome is condensed
- 2 sister chromatids join at the centromere to form a chromosome
what is a nucleosome?
DNA wrapped around histone proteins
what is a chromatin?
lots of nucleosomes (DNA wrapped around histone proteins) packed together to form chromatin
what is a chromatosome?
- nucleosome and 1 histone protein
what is a chromosome
packaged DNA wrapped around histone proteins carrying genetic information
- 2 sister chromatids form a chromosome
what is a chromatid?
- one of the 2 identical halves of a chromosome that has been replicated for cell division
what is the human genome split into?
- nuclear genome
- mitochondrial genome
what is the nuclear genome split into?
- genes and gene-related sequences (30%)
- extragenic DNA (70%)
what is genes and gene-related sequences split into?
- coding DNA
- non-coding DNA
what is non-coding DNA split into?
- 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
what is extragenic DNA and what is it split into?
- DNA between genes
- split into repetitive DNA and unique/low copy number
what is repetitive DNA split into?
- tandemly repeated DNA
- interspersed genome-wide repeats
what are the 3 types of tandemly repeated DNA?
- satellite
- minisatellite
- microsatellite
what are the 4 types of interspersed genome-wide repeats?
- LTR elements (long terminal repeats)
- LINEs (long interspersed retrotransposable elements)
- SINEs ( short interspersed retrotransposable elements) - DNA transposons
what are DNA transposons?
= 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
what are the 6 components to a typical gene?
- 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
how is DNA altered to produce mature mRNA?
- add 5-methyl guanosine cap and 3’ poly-A tail
- remove introns (splicing)
what are exons?
- coding part of DNA and mature mRNA
- codes for proteins
what are introns?
- non-coding part of coding region of DNA
- removed via splicing to form mature mRNA
generally in DNA, are there more introns or exons?
- more introns than exons
whats the relationship between proportion of introns and size of gene?
- the larger the gene, this bigger the proportion of introns
- the larger the gene the smaller the proportion of exons
what are genes within genes?
you can get small genes within introns of larger genes
describe the relationship between gene densities and size of region
- the larger the number of bases, the lower the gene density
what are some different features of gene families?
- 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)
describe the length and location of satellite DNA
- 100kb to 5Mb
- repeat = 5bp-5kb
- locations = heterochromatin (regions of genome that are gene poor and very variable), particularly at centromeres
describe the length and location of minisatellite DNA
- 0.1-20kb
- repeats = 6-64bp
- scattered but concentrated near telomeres
describe the length and location of microsatellite DNA
- <100 bp
- repeats = 1-5bp
- dispersed throughout genome
describe a use of satellite DNA
- 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
describe ultracentrifugation of satellite DNA
- 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
give some examples of dispersed repetitive DNA
- 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)
why do mitochondria have their own DNA?
- 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
describe the structure/differences of mitochondrial DNA
- 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
what is the mutation rate of mitochondrial DNA vs nuclear DNA?
much higher mutation rate of mitochondrial DNA than nuclear DNA as mitochondrial DNA produces a lot more free radicals
how does the size of mitochondrial DNA compare to nuclear DNA?
- mitochondrial DNA is much smaller
- 1/180,000 the size of nuclear genome
how does mitochondrial DNA coding compare to nuclear DNA coding?
- 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
what is the pattern of mitochondrial inheritance?
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
