2.1 Genomes Flashcards
What are two important definitions of a genome?
How big is the human genome?
About 3.2 billion bases or 25,000 genes
What is the C value paradox?
- C value is the total amount of DNA in the genome
- It is expected that the more complex the organism, the more DNA is needed to run it. So expect a linear relationship between genome size and organism complexity.
- The C value paradox is that in most complex organisms there doesn’t appear to be the expected relationship between complexity and genome size because larger organisms have more repetitive sequences or junk DNA
How does gene density vary between species?
- If you compare a 65kb region of 4 organisms, genes are packed tight in bacterial and yeast genomes and slightly less in drosophila genome
- In humans genes only comprise a small fraction of the whole. Most is intergenetic DNA (transposons) on intronic DNA
What is a gene?
Region of DNA that is transcirbed as a single unit and carries information for a discrete hereditary characteristic. Usually corresponds to a single protein or single functional RNA (rRNA tRNA)
What is the difference between the 5’ end and the 3’ end of DNA?
Each DNA strand has two ends. The 5’ end of the DNA is the one with the terminal phosphate group on the 5’ carbon of the deoxyribose; the 3’ end is the one with a terminal hydroxyl (OH) group on the deoxyribose of the 3’ carbon of the deoxyribose
What is the difference between exons and introns?
What are the 5’ and 3’ untranslated regions? UTRs
5’ UTR = the region of mRNA before the START codon.
3’ UTR = the region of the mRNA after the STOP codon.
How do pseudogenes normally arise?
- Say for example the B-Globin gene gets duplicated and incorporates itself on another part of the chromosome
- As there is still a funcitoning B-globin gene the new one can still undergo changes and mutations without selection
- Mutations could affect promotor (affecting expression), coding sequence (non sense mutations), spicing sites
- This dysfunctional copy is now called a pseudogene
How do processed pseudogenes differ from conventional ones?
- A gene has been transcribed to produce mRNA which is processed and mature
- Reverse transcriptase makes a DNA copy of mRNA
- Double stranded DNA version inserts elsewhere in the genome.
- Results in a processed pseudogene but is still non functional becuase it does not have promotor etc
How are gene fragments created?
Processed pseudogenes that aren’t under selective pressure get moved around. These non functional genes can be broken up by chromosomal rearrangements
What are tandem repeats?
Repeated end to end copies of a short DNA sequence
What are microsatellites?
Tandem repeats of very short (1-6 bp) of DNA sequence, total array size 10-150 bp
What are mini satellites?
Tandem repeats of short (7-100 bp) of DNA sequence with total array size 100-20,000 bp
What are some examples of tandem repeats?
- CA repeat makes up 0.25% of the human genome
- Centromeres have the alpha satellite DNA (171 bp motif)
- Telomeres have GGTTA
What are transposons?
They are parasitic genetic elements that can move about the genome. Sometimes called “jumping genes”
What are some diseases caused by transposons?
- Haemophilia caused by insertion of the retrotransposon L1 into the Factor IX gene.
- Muscular dystrophy caused by a L1 insertion into Dystrophin gene.
What are the two ways transposons move?
- Conservative transposition (cut/paste)
- The transposon is excised from its original position (often leaving a characteristic mark) and inserts at a new location.
- Replicative transposition (copy/paste)
- The transposon inserts at a new location but the original copy remains
What are the two main classes of transposon?
What are the general features of a DNA transposon?
- You need a gene that it encodes, which is the enzyme that helps it move around
- Transposase - an enzyme involved in movement of a DNA transposon
- ITR - Inverted terminal repeat, a palindromic sequence involved in movement
- TSD - target site duplication, genomic sequence duplicated during insertion
What are the steps for a DNA transposon to be moving around?
- Transposase gene is transcribed and translated to make the Transposase protein
- Transposase enzyme binds to ITRs
- The transposase enzyme catalyses the excision of the transposon from its original site.
- The transposase enzyme catalyses the insertion of the transposon into a new site
What are the types of retrotransposons?
What is the mechanism of retrotransposon movement?
- Retrotransposon is transcribed.
- translation creates reverse transcriptase
- Reverse transcriptase synthesises the reverse stranf (in DNA) using RNA as a template.
- 2nd DNA strand is produced
- retrotransposon inserts into new chromosomal position
