Term
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Definition
| There is not a strong correlation between organism complexity and genome size |
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Term
| Bacterial genomes: range of size |
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Definition
| 580 kb to 13 Mb, thus there is 20-30 fold size variation within prokaryotes |
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Term
| Eucariotic genomes: range of size |
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Definition
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Term
| Is there a correlation between genome size and gene number? |
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Definition
In bacteria, yes.
In eukaryotes, no. |
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Term
| How C-value paradox can be explained? |
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Definition
| most of the C-value variation is due to the amount of non-coding DNA |
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Term
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Definition
| Large regions of the genome with no (or very few) gene |
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Term
| Correlation between genome size and coding DNA |
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Definition
| there is a steep decline in the fraction of genic DNA (coding DNA) as genomes become larger |
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Term
| Main features of satellite DNA: GC content, length, place |
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Definition
- repeated sequences that have either high GC (heavy) or high AT (light) content
- short sequences (2-2000 bp) repeated 1000’s of times
- heterochromatic regions and around centromeres |
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Term
| Main features of MINIsatellite DNA: GC content, length, place |
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Definition
- 9-100 bp repeated 10-100 times
- subtelomeric regions and (rarely) dispersed throughout chromosomes |
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Term
| Main features of MICROsatellite DNA: GC content, length, place |
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Definition
- 1-5 bp repeated 10-100 times
- dispersed throughout chromosomes, often in and around genes |
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Term
| What is the mutation rate in MICROsatellites? How one could use it? |
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Definition
| High, “DNA fingerprinting” |
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Term
| Which diseases are associated with increase in repeat number in microsattelites? |
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Definition
Fragile
-
X syndrome (CCG)
Huntington’s disease (CAG)
Schizophrenia (CAG)
Myotonic Dystrophy (CTG) |
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Term
| Transposable elements: definition, number in human genome |
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Definition
-Pieces of DNA that can move within the genome and increase in number.
- 50% of the human genome |
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Term
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Definition
| transposons and retrotransposons |
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Term
| Conservative transposition mechanism of transposition |
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Definition
- moves from one place to another
- does not necessarily lead to an increase in copy number
- Copy number increased through recombination between chromosoms
- equal number of gains and losses |
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Term
| Replicative transposition mechanism of transposition |
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Definition
| copy number is increased:original element remains at donor site,new copy inserts into a new site,“copy-and-paste” |
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Term
| Retrotransposition mechanism of transposition |
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Definition
-TE is transcribed into RNA, then reverse transcribed into cDNA, then inserts
- copy number increases
- the most abundant in a genome. |
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Term
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Definition
| Have inverted repeats at ends, encode a single gene (transposase), can move by themselves |
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Term
| non - autonomous transposons |
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Definition
- have inverted repeats at ends, but no transposase gene
-Can not move by themselves
- can move if there is another element in the genome producing transposase |
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Term
|
Definition
- no inverted repeats
-transposase gene
- can not move
- can cause non-autonomous elements
to move |
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Term
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Definition
| have intact promoter, are transcribed, and can retrotranspose |
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Term
| Dead or dead On Arrival (DOA) retrotransposons |
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Definition
- truncated at the 5’end when inserting into DNA
- lose promoter
- no longer can be transcribed or retrotranspose
- junk DNA, no selection |
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Term
| Definition of pseudogenes |
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Definition
Previously functional genes that have lost their function due to mutation (stop codon into the ORF or an insertion/deletion)
- lose function due to parasitic or symbiotic relationship |
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Term
| Unprocessed pseudogenes: how occurred |
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Definition
- arise through tandem duplication(during dna replication)
- usually adjacent in the genome
- other copy may accumulate mutations and become a non-functional pseudogene |
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Term
| Processed pseudogenes (retrotransposed genes): how occurred |
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Definition
- the mRNA of a nuclear gene is reverse transcribed into cDNA, then reinserts
- uses the reverse transcriptase and integrase enzymes
- does not have introns present in the parental gene
- If recent, may have a poly(A) sequence at 3’ end
- lacks promoter sequences |
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Term
| Why retrotransposed genes occur? |
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Definition
1) Expression level,highly expressed genes have a greater chance of being reverse transcribed
b) Gene size: short mRNAs may retrotranspose better than long mRNAs
c) Sequence specific: the primary sequence of some genes may be better for retrotransposition |
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Term
| Why is there such great variation in genome size? |
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Definition
a) adaptive–the non-coding DNA is important to the organism.
b) junk DNA -most of the non-coding DNA serves no purpose |
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Term
| C-value paradox explanation for Hawaiian crickets and Drosophilla |
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Definition
- Drosophila genome is small and has almost no pseudogene, crickets - vice verca
- Spontaneous DNA loss is faster in Drosophila
- pseudogenes are lost very rapidly by deletion mutations |
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Term
| C-value paradox explanation for grasshoppers and Drosophilla |
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Definition
- Drosophila genome is small and has almost no pseudogene, grasshoppers - vice verca
- Grasshoppers have a very low rate of DNA loss
- In Grasshoppers there are many pseudogenes in the nuclear DNA derived from mitochondrial genes (NUMTs)
- NUMTs are non functional |
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Term
| Why are NUMTs non-functional? |
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Definition
a) the genetic code is different between mitochondria and nucleus
b) they often lack a promoter
c) they do not have a signal sequence to target them to mitochondria |
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Term
| Correlations between deletion size and genome size for flys, crickets and grasshoppers |
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Definition
Deletion size:Dros > Lau > Pod
Genome size: Pod > Lau > Dros |
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