Genomes

Question 1

Biology and reverse engineering similarities?

Answer 1

• Similar process:
  
  • Read the information (essential for understanding the genetic program)
  • Separate and annotate the different parts
  • In particular separate logic and data
  • Make hypothesis and try to prove them by changing parts
  • Try to understand the entire program or project

Question 2

Reading assembly of genomic sequences

Answer 2

• cost for producing DNA sequences is quite low
• reading the full assembly is still computattionally difficult (de novo assembly)
  
  • limited to resequencing with reference genome

Question 3

Prokaryotes

Answer 3

• Biological organisms, bacteria and archea
  
  • unicellular, simple structure
• bacterium size is about 1μm, a typical Eukaryotic cell is 10-20 times bigger
• exchange their genetic information (DNA) amongst individuals
  
  • sex pilus, in critical conditions
  • generally they duplicate [clones]
• haploid, one copy of the genome per cell

Question 4

Eukaryotes

Answer 4

• Complex organisms, plants, animals and some unicellular organisms [yeast, protozoa]
  
  • often multi-cellular, different compartments
  • during cellular division DNA is condensed and forms chromosomes
• exchange their genetic information (DNA) amongst individuals
  
  • reproduce sexually
  • alternate haploid and diploid stages
  • fertilization: two haploid cells merge and become one diploid cell
• predominantely diploid, two copy of the genome per cell [one for parent]

Question 5

Mitosis and Meiosis

Answer 5

• Mitosis is the process with which diploid cells duplicate
  
  • same genomic DNA
• Meiosis occurs when a diploid cell produces haploid cells, gametes
  
  • crossing over is a process where there is an exchange od DNA between homolougous chromosomes (no mutations)
    
    • human, the probability of a crossing over within any two loci at a distance of 1 million bases is about 1% per generation

Question 6

What is a loci?

Answer 6

• In genetics, a locus (plural loci) is a specific, fixed position on a chromosome where a particular gene or genetic marker is located

Question 7

Diploid vs haploid

Answer 7

• diploid allows to maintain a much larger pool of variant genes, most of these mutated genes do not work as well as the original, but together with other mutations may improve the fitness
• some organisms (yeast) have very similar haploid and diploid cells

Question 8

What are the key points for genetic diversity and evolution?

Answer 8

• Mutations, accumulation of mutations generates diversity
• DNA recombination, may combine together useful mutations from different individuals
• Diploidy, high level of diversity in individuals [heterozygousity] and population
  
  • if one gene variant [alleles] does not work there are others that do
  • kept, genetic diversity in population is good and may turn good in the future if combined with other genes or if environment changes

Question 9

Heterozygous vs homozygous

Answer 9

• Heterozygous status, when a locus is occupied by two different alleles
  
  • ok if one of the two genes is functional [recessive mutation]
• Homozygous status, locus occupied by same bad alleles
  
  • diploidy, generally does not happen

Question 10

Gene prediction in prokaryots

Answer 10

• Can be done considering the genetic code

Question 10

Gene prediction in prokaryots

Answer 10

• Can be done considering the genetic code
  
  • 64 possible codons
  • 3 stop codons
  • ATG start codon
• sequence encoding proteins -> no stop codons
  
  • random sequence, stop codon every ~21 codons (64/3)

Question 11

Gene prediction in eukaryotes

Answer 11

• more difficult
  
  • introns (intragenic region, non-coding regions) are present, interrupt genes
  • removed in mRNA via splicing [only exons (encoding regions) are kept]
• <2% of gene is coding sequences
• non-coding regions (98% of human genome) could contain assembling informations and operating instructions

Question 12

Why there is cell differentiation while all animals share the same genes?

Answer 12

• stem cells can generate many differentiated cell types
  
  • each one has a specific set of expressed genes
  • set of nuclear genes remains the same
• to create a new cell with new characteristics new genes are not necessary
  
  • change pattern of expression often works

Question 13

What is a genome?

Answer 13

• It consists of all of the DNA contained in a cell’s nucleus
  
  • total number of bases in one representative copy of its nuclear DNA
  • for diploid organisms, sum of the sizes of one copy of each chromosome pair
• Organisms differ in their genome sizes

Question 14

How to sequence genomes?

Answer 14

• large, end-to-end read in a single step is not possible
• DNA must be broken down into smaller pieces
  
  • each piece is then processed with chemical reaction to identify order and type of bases [sequence read]
  • sequence reads are assembled back together to deduce the sequence of the starting genome
• for human genomes there are reference sequences available [computational assembly process]

Question 15

shotgun sequencing vs whole-genome sequencing

Answer 15

• shotgun sequencing
  
  • the process of breaking down genomes, sequencing the individual pieces of DNA and reassembling
• whole-genome sequencing
  
  • sequencing of an entire genome
  • an alternativeis a targeted sequencing of part of a genome (generally exons)
  • whole-exome sequencing (requires extra manipulation)