Chapter 2 long questions

Question 1

Discuss the two approaches that can help us in understanding the human genome

Answer 1

Comparative genomics:
- e.g compare the human and chimp genomes
- ask how differences between these genomes might give rise to differences between the species

Study of human mutations
- many mutations alter phenotypes and give clues to the functions of affected regions, many mutations cause disease
- Affected regions may encode structural proteins or enzymes or regulatory proteins or RNAs or they may be DNA sequences that are targets of regulatory mechanisms
- Understanding the effects of such mutations will illuminate human biology and often have immediate clinical applications

Question 2

Briefly describe what comparative genomics has discovered when comparing human and chimp genomes

Answer 2

• Genome are about 96% identical, focus on the 13Mb that’s different rather than the full 3.2Gb
• Humans and chimps express similar proteins, homologous proteins are identical or very similar
  > 30% of human vs chimp proteins show no difference at all
  > more or less 2 amino acids differ where there are differences

How do humans and chimps develop differently
- Regulation of gene expression is different
- the 4% sequence variation make profound differences in phenotype suggest a chaotic system, whereby a small disturbance can lead to large changes in subsequent trajectory

Question 3

Understand the info relating to restriction enzymes, including sticky vs blunt ends, palindromes, restriction fragments, determining average fragment lengths as well as the relevance of mutations to restriction enzyme digestions

Answer 3

• Restriction enzymes are commonly used in DNA profiling: HaeIII (blunt), HinfI (sticky) and TaqI (sticky)
• Palindromes reads the same from 5’ to 3’ and 3’ to 5’
• Cleaving DNA produces restriction fragments
• Fragment lengths can distinguish between different DNA molecules
• Analysis through gel electrophoresis can enable restriction map
• Mutations in restriction sites:
  > there may be repetitive stretch of DNA (presenting variable lengths between individuals) between restriction sites - VNTRS. Variation yields RFLPs separated by gel electrophoresis the southern blotting

Question 4

DNA fingerprinting - the roles of VNTRs vs RFLPs vs PCR; using DNA fingerprinting to determine family relationships, e.g. parentage

Answer 4

VNTRs ( Variant number tandem repeats)
- Most commonly uses in paternity testing
- 15 - 20 loci
- Shared between mother, father and child = uninformative
- Share between fate and child (not mother) = strength of paternity inference varies with the frequency of the appearance in the population.
- Paternity index is calculated

RFLPs (Restriction fragment length polymorphisms)
- Main disadvantage is that it requires large amounts of undegraded DNA (10-15 ng, 20-25kb)

PCR (Polymerase chain reaction)
- Uses tiny amounts of DNA to amplify as little as 100bo
- Currently used to target STRs
- Amplification produces 200-500 bp fragments.