Week 2 Flashcards
_______ is the science of genes, heredity, and the variation of organisms.
Genetics
_______________ attempts the study of large scale genetic patterns across the genome for a given species. It deals with the systemic use of genome information to provide fide answers in biology, medicine, and industry
Genomics
___________ estimated cost 3 billion dollars and it took 15 years. It began in 1988 and the first draft was announced in 2000 with the more complete eversion released in 2003
Human genome project
____________
is the reeecniquea used for the human genome project
Shotgun sequencing
What is the first step of shotgun sequencing?
- break the genomic DNA into pieces
- cloning into plasmid vectors
- collection of clones=library
- transformation to E coli
Library generation
Question? Why do we need to introduce ecoli into the library regeneration
To replicate or amplify the library i.e. asexual reproduction
What is the second step of shotgun sequencing?
Template preparation
Why do we use antibiotic for select plasmids during template preparation
it makes the cell it is injected with resistant to antibiotics
What is the third and final step of shotgun sequencing?
DNA sequencing
*chain termination DNA sequencing
The DNA sequencing in shot gun sequencing is similar to _________________
PCR reaction
The reaction mix requires: template DNA, Taq polymerase, dNTPs, ddNTPs, and a primer
How hod ddNTPs work as terminators of DNA sequencing?
Because they lack hydroxyl groups, it is missing the 3’ hydroxyl group. Without this group, they can not be extended.
___________: containing all four of the standard dNTPs and the DNA polymerase template DNA and primer
sequencing reactions
During DNA replication there needs to be a higher concentration of dNTPS as apposed to ddNTPS why?
You dont want your sequence to terminate prematurely. Higher levels of dnTPS allow for more extension of DNA molecules
What are the two conditions that must be satisfied to have DNA products of all sizes
- more dNTPS than ddNTPS
- adequate materials (primers, polymerases)
_________ is used on DNA fragments to determine size.
Gel electrophoresis
Traditionally the mix of sequencing reactions (DNAs) is run on a denaturing ___________ which can resolve bands differing in size by _________
page gel
1 nucleotide
*based on their size they will be in different locations of the Gel
What is is called if you did not cover all the nucleotides? What is this called? How is it fixed?
This is called a sequencing error. This is fixed using an arbitrary value/ variable such was N. Then we use statistical modeling to find N
What is the fourth step of shotgun sequencing?
-needs overlapping sequence,
requires 7-9x coverage of the human genome (3 billion bases -> needed 21-27 billion bass to provide adequate fragment overlap)
Assembling fragments
What is the fifth step shotgun sequencing?
Generation of open reading Frame -> homology searches
-> putative ID frameshift detection -> function assignment metabolic pathways gene families -> DNA molds regulatory elements repetitive elements -> comparative egenoimisc
Annotation
*comparative genomics
_____________ shows a table of different gnome and how they differ between species
genome size comparison
___________ the era of science that we are currently in is large scale sequencing which has become quite routine. The next challenge in genomics in deciphering the sequencing data
post sequencing era
Different types of gene finding
- RNA genes: tRNA, rRNA, snoRNA, snRNA, microRNA
- protein coding genes:
__________:
contains no introns, simpler regulatory features
prokaryotic protein coding genes
__________:
- exon intron structure
- complex regulatory features
eukaryotic
