Omics Flashcards
1
Q
describe SSRs
A
- simple sequence repeats
- di, tri, or tetra nucleotide repeats are called SSR
- slightly longer repeats are called VNTR
2
Q
describe low copy repeats
A
- may be very long; thousands of base pairs
3
Q
describe transposons
A
- LINES
- LINES encode reverse transcriptase – jumping genes
- SINES
- the Alu sequence is found in SINES
4
Q
name the 3 general types of pseudogenes
A
- vestigal genes (now dormant)
- duplicated genes that are not expressed
- processed pseudogenes
5
Q
name an example of a vestigial gene
A
- Humans have the gene for vitamin C formation, however, it doesn’t function
- it was never duplicated
6
Q
name an example of a duplicated gene
A
- an example of a duplicated and turned off gene: one of the globin genes in the B-globin locus
- it was duplicated and now it is not expressed
7
Q
describe the formation of a processed pseudogene
A
- introns are removed from the primary transcript by normal splicing
- reverse transcription and integration then yield a processed pseudogene which does not contain introns
- the processed pseudogene is flanked by short direct repeats of target-site DNA that were generated during its integration
- there are ~8000 in the human genome
8
Q
name the 2 ways transposons may lead to disease
A
- transposons (jumping genes) may integrate into a critical spot in the genome, disrupt a gene and cause disease
- transposons as repetitive sequence may lead to misalignment during meiosis and gene disruption
9
Q
describe repeating DNA used in forensics
A
- DNA samples for crime investigations and paternity issues use highly polymorphic single locus regions such as the SSR or VNTR loci
10
Q
describe SSR/STR/VNTR PCR genotyping
A
- it is an example of multiplex PCR
- many (much more than 3) loci may be genotyped in a single multiplex PCR reaction
- in this case multiplex means that more than one primer pair is being used in each reaction
11
Q
describe gene duplication
A
- gene duplication (aka chromosomal duplication) can occur by error in homologous recombination, a retrotransposon event or duplication of an entire chromosome
- in duplicated genes the second copy is free from selective pressure
- mutations can accumulate without losing gene function
- gene duplication is thought to be the engine of evolution
12
Q
describe genetic basis behind R-G color blindness
A
- explained by unequl intragenic recombination between a pair of X chromosomes during meiosis
- normal individuals have 1 red pigment gene and either 1, 2 or 3 green pigment genes on their X-chromosome
- 2 normal X-chromosomes line up incorrectly and undergo unequal meiotic crossing over
- an X-chromosome is formed that is missing green gene
13
Q
describe gene duplication and α-thalessemia
A
- there are multiple globin genes found in clusters on chromosomes 11 and 16
- these sites probably arose due to gene duplication
- chr 16 contains the α-cluster
- because of the repetitive structure of the α-cluster, deletions are the common disease causing mechanism for α-thalessemia
14
Q
define haplotype
A
- haplotype is a combination of alleles at different chromosomal loci that are transmitted together
- the HapMap allows genetic variation analysis without individual genome sequencing
- it is a catalog of common genetic variants that occur in humans
15
Q
describe GWAS
A
- an attempt to uncover genetic determinants of multifactorial diseases
- GWAS is created by scanning 1000s of SNP among 1000s of people
- searches for genetic variation associated with a particular disease
