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Briefly describe the structure of chromosomes
made of chromatin (DNA protien complex)
p= short arm
q = long arm
joined at centromere
Euchromatin = light packed, undergoes transcription
Heterochromatin = tight packed, no transcription
See bands with Giemsa stain (binds AT rich DNA)
what is the principle of genome projects?List 2 different Genome projects and their main differences
Principle; genomic DNA - BAC (bacteria artificial chromosome) library - Contigs - Map - shotgun clones
Public - international sequencing consortium (1990)
-BAC library up to 2 million bp insert size
- shotgun sequence each BAC clone and assemble sequence
Private - Celera (1999)
-shotgun library 500-800 bp insert)
- random sequencing of clones
- supercomputer to assemble
What kind of techniques were used in early genome projects?
Traditional Nucleotide sequencing
Manual Dideoxy - PCR many diff length frag
Automated/Flourescent - each ddNTP has fluro tag in single tube
Automated dideoxy - capillary w fluro tag
What are some of the findings of the human genome project?
genome = 3.3 billion bp
20500 genes
avg mRNA = 2500 bp
<2% of genome is exons
50% is repetitive DNA
~75000 bases between genes
~2500 protien coding sequence mRNA
99% of sequence is identical in all people
What are the differences between Autonomous and Non-autonomous repetitive DNA in the genome
Autonomous - LINES (6-8 kb), retrovirus like LTR transposons 6-11 kb, DNA transposon 2-3 Kb
Non-Autonomous - SINES (100-300bp), Retrovirus like LTR transposons 1.5-3kb, DNA transposons 80b-1.5kb
What groups were studied in the 1000 genomes project?
Asian, European, African, American
whole genome 180 samples
whole genome of 2 mother/father/adult/child
1000 gene regions in 900 samples
What did the 1000 genomes project find?
95% of genome variants are common
each person has 250-300 loss of functional variants
80-100 variants in inherited disorders
87.4 SNPs, 36 Million short insertions/deletions
60k structural variants all phased into high quality halotypes
Name the 3 types of nucleotide variation and their properties
VNTR - 15-100 base repeats
array length - 100b-20kb on telomeres
only between genes, can be extracted with restriction enzymes
changes through unequal chromosome recombination
STR - 1-4 base repeats
array length <100b waidley distributed in euchromatin
can acquire changes through slipping
SNPs - 1 nucleotide (must occur in >1% of pop)
1 in 500 bases
can be detected with allele specific PCR (specific primers, only template with the SNP is seen in electrophoresis)
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