Week 3

Question 1

Model organisms (2 points)

Answer 1

• easy to maintain and breed in laboratory

- relatively small genomes

Question 2

Vector dephosphorylation

Answer 2

Phosphate overhanging make phosphodiester bond with other strands of DNA with ligase

Question 3

Direct cloning

Answer 3

Cuts with two restriction enzymes. Odd ends allow it to bind to other sites

Question 4

Blue/White screening

Answer 4

Media cleaved, turning blue, when plasmid that responds to it is present

Question 5

cDNA

Answer 5

From mRNA, reverse-transcription. Can represent all mRNA in wanted area of study

Question 6

Synthetic DNA

Answer 6

Chemical gene synthesis

Question 7

TA cloning basics

Answer 7

Di-deoxi-TTP finishes the reaction

Question 8

Gateway cloning

Answer 8

Clone PCR products into a vector (lysogenic pathway, for example)
Re-sequencing and further PCR after initial is unneeded

Question 9

Gibson assembly enzymes (3 points)

Answer 9

Exonuclease
DNA polymerase
DNA ligase

Question 10

Gibson Assembly Steps basics

Answer 10

Exonuclease chews back 5’ ends of DNA, fragments annealed and 3’ end extended.

Question 11

e-value

Answer 11

Number of alignments expected by pure chance

Question 12

p-value

Answer 12

probability alignment with that score occurring by chance

Question 13

Database problems (2 points)

Answer 13

• Quality of data (from different expertises)

- Annotation (minima and automated)

Question 14

Multi-sequence alignment

Answer 14

Summarise sequence relationships to identify and characterise gene/protein families.
Structural prediction.

Question 15

Motifs/patterns (2 points)

Answer 15

Regions of conserved amino acids and important proteins

Question 16

Annotations (4 points)

Answer 16

Predicted cellular location, function, structure, processing sites

Question 17

CLUSTALW

Answer 17

Develops relationship between sequences.

Find homologous sequences

Question 18

Node

Answer 18

Most common ancestor

Question 19

Clades

Answer 19

Groupings coming from one common ancestor

Question 20

Rooted phylogenetic trees

Answer 20

Uses outgroup

Question 21

Unrooted phylogenetic trees

Answer 21

No ancestral outgroup

Question 22

Synteny

Answer 22

Deduction that two or more genomic regions are derived from a single ancestral genomic region

Question 23

Syntenic

Answer 23

Occurs on same chromosome

Question 24

Regulatory Regions

Answer 24

Evolution is slow due to conservation and importance to gene expression

Question 25

Genome-wide association study (GWAS) (4 steps)

Answer 25

Collect DNA, identify SNPs, manhattan plot , identify candidate genes for association studies.