Lab 9 and other questions

Question 1

bioinformatics

Answer 1

a combination of molecular biology and computer science that aims to develop the technology for organizing, analyzing, and storing sequence data

Question 2

Difference between accuracy and precision?

Answer 2

Accuracy- close to true value
Precise- close to each other

Question 3

What are you digesting?

Answer 3

Sample DNA

Question 4

Do you understand plasmid and linear DNA restriction/ligation? See Extra Help, Lab 6 folder

Question 5

What are we ligating? What products could form during ligation

Answer 5

Sample DNA and plasmid. Recombinant/nonrecombinant plasmid

Question 6

What are the steps of transformation? (What happens at 42ºC?

Answer 6

heat shock

Question 7

Can also have E.coli with nonrecombinant plasmid or no plasmid… how do we distinguish?

Question 8

How and why do we purify our products? Hint: compare PCR and Sequencing Reactions

Question 9

Purpose of Alkaline Phosphatase?

Answer 9

Remove phosphate groups, ______________-

Question 10

What are the sequencing reagents? Purpose of each reagent?

Question 11

Purpose of Blastn?

Answer 11

Nucleotide search and alignment program

Question 12

Blastx?

Answer 12

Protein database

Question 13

Blat?

Answer 13

DNA search to find homologs between closely related species (fast, but less accurate than blastn/x)

Question 14

annotate the gene sequence

Answer 14

RNA and amino acid sequences it encodes are determined

Question 15

comparative genomics,

Answer 15

information such as the sequence, function, and location of a gene are evaluated across different species

Question 16

homologous.

Answer 16

genes that are evolutionarily related to one another

Question 17

How does Sanger Sequencing work?

Answer 17

1. template DNA is targeted using a sequencing primer.
2. Primer binds to DNA adjacent to region of interest.
3. Chemical analogs of the four nucleotides in DNA are used.
4. DNA replication occurs, and the sequence of nucleotides is determined.

Question 18

Why add a really rich broth?

Question 19

What happens at 37ºC?

Answer 19

Bacteria recover, replicate the new DNA (plasmid), and express the desired gene

Question 20

How do you calculate TE? What does TE tell us?