Week 3 Flashcards
Model organisms (2 points)
- easy to maintain and breed in laboratory
- relatively small genomes
Vector dephosphorylation
Phosphate overhanging make phosphodiester bond with other strands of DNA with ligase
Direct cloning
Cuts with two restriction enzymes. Odd ends allow it to bind to other sites
Blue/White screening
Media cleaved, turning blue, when plasmid that responds to it is present
cDNA
From mRNA, reverse-transcription. Can represent all mRNA in wanted area of study
Synthetic DNA
Chemical gene synthesis
TA cloning basics
Di-deoxi-TTP finishes the reaction
Gateway cloning
Clone PCR products into a vector (lysogenic pathway, for example)
Re-sequencing and further PCR after initial is unneeded
Gibson assembly enzymes (3 points)
Exonuclease
DNA polymerase
DNA ligase
Gibson Assembly Steps basics
Exonuclease chews back 5’ ends of DNA, fragments annealed and 3’ end extended.
e-value
Number of alignments expected by pure chance
p-value
probability alignment with that score occurring by chance
Database problems (2 points)
- Quality of data (from different expertises)
- Annotation (minima and automated)
Multi-sequence alignment
Summarise sequence relationships to identify and characterise gene/protein families.
Structural prediction.
Motifs/patterns (2 points)
Regions of conserved amino acids and important proteins
Annotations (4 points)
Predicted cellular location, function, structure, processing sites
CLUSTALW
Develops relationship between sequences.
Find homologous sequences
Node
Most common ancestor
Clades
Groupings coming from one common ancestor
Rooted phylogenetic trees
Uses outgroup
Unrooted phylogenetic trees
No ancestral outgroup
Synteny
Deduction that two or more genomic regions are derived from a single ancestral genomic region
Syntenic
Occurs on same chromosome
Regulatory Regions
Evolution is slow due to conservation and importance to gene expression
