Omics

Question 1

describe SSRs

Answer 1

• simple sequence repeats
  
  • di, tri, or tetra nucleotide repeats are called SSR
  • slightly longer repeats are called VNTR

Question 2

describe low copy repeats

Answer 2

• may be very long; thousands of base pairs

Question 3

describe transposons

Answer 3

• LINES
  
  • LINES encode reverse transcriptase – jumping genes
• SINES
  
  • the Alu sequence is found in SINES

Question 4

name the 3 general types of pseudogenes

Answer 4

1. vestigal genes (now dormant)
2. duplicated genes that are not expressed
3. processed pseudogenes

Question 5

name an example of a vestigial gene

Answer 5

• Humans have the gene for vitamin C formation, however, it doesn’t function
  
  • it was never duplicated

Question 6

name an example of a duplicated gene

Answer 6

• 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

Question 7

describe the formation of a processed pseudogene

Answer 7

• 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

Question 8

name the 2 ways transposons may lead to disease

Answer 8

1. transposons (jumping genes) may integrate into a critical spot in the genome, disrupt a gene and cause disease
2. transposons as repetitive sequence may lead to misalignment during meiosis and gene disruption

Question 9

describe repeating DNA used in forensics

Answer 9

• DNA samples for crime investigations and paternity issues use highly polymorphic single locus regions such as the SSR or VNTR loci

Question 10

describe SSR/STR/VNTR PCR genotyping

Answer 10

• 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

Question 11

describe gene duplication

Answer 11

• 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

Question 12

describe genetic basis behind R-G color blindness

Answer 12

• 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

Question 13

describe gene duplication and α-thalessemia

Answer 13

• 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

Question 14

define haplotype

Answer 14

• 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

Question 15

describe GWAS

Answer 15

• 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

Question 16

name problems associated with GWAS

Answer 16

• data may not be complete–rare variants won’t be found
• correlation does not mean causation

Question 17

define transcriptome

Answer 17

• all mRNA in a particular cell under a particular condition
• use of cDNA microarrays determine the genes expressed
• allows comparison of expressed genes between normal and diseased states

Question 18

define proteomics

Answer 18

• an attempt to look at the protein fingerprint of a biological sample
• the number of genes does NOT equal the number of proteins because genes can have:
  
  • multiple start sites
  • alternate splicing
  • RNA editing