Week 2 Material

Question 1

Define Isoschizomers

Answer 1

• Are pairs of restriction enzymes specific to the same recognition sequence
• Ex: Sphl (CGTAC/G) & Bbul (CGTAC/G)

Question 2

How do bacterial protect their own genomic DNA from restriction enzmyes?

Answer 2

-Through methylation or addition of functional groups to certain base pairs. Some enzymes like methylase add methyl groups to protect

Question 3

Define Neoschizomers

Answer 3

• Are pairs of restriction enzymes that are specific to the same recognition sequence but that cut differently
• Ex: Smal (CCC/GGG) & Xmal (C/CCGGG)
• Ex: Kpn1 (GGTAC/C) & Acc651 (G/GTACC)

Question 4

Gel electrophoresis separates molecules by?

Answer 4

-Charge, size and shape (circular, double, linear etc)

Question 5

Is the length of a protein contributing to the charge like DNA?

Answer 5

-No, the R side groups have different properties which affect its (-) charge

Question 6

What is the function of SDS?

Answer 6

• SDS denatures the proteins and adds sulfate group to parts of the protein. These parts will contribute to an overall (-) charge which will push it through the gel once power is turned on.
• Note the larger the size, more sulfate groups are added.

Question 7

Source, Gel cast, Uses, and separation of large or small molecules of Agarose

Answer 7

• Source: Polysaccharide derived from seaweed
• Gel cast: Horizontally
• Used for: DNA & RNA
• Separation of large or small?: Both but especially good for resolving large molecules

Question 8

Source, Gel cast, Uses, and separation of large or small molecules of Polyacrylamide

Answer 8

• Source: Cross linked polymer of acrylamide (potent neurotoxin)
• Gel cast: vertically
• Used for: DNA, RNA, and protein
• Separation of large or small?: Both but especially good for resolving small differences in molecular weight.

Question 9

What is the function of Southern blot?

Answer 9

-Enable researchers to identify a specific DNA molecule in a complex mixture of DNA molecules

Question 10

What is the function of northern blots?

Answer 10

-Enable researchers to identify a specific RNA (mRNA) molecule in a complex mixture of RNA molecules

Question 11

What is the function of western blots?

Answer 11

• Also called immunoblots
• Enable researchers to identify a specific protein in a complex mixture of proteins
• Use an antibody probe to detect a target protein

Question 12

Why is the 3’OH oligonucleotide primer important? (What happens chemically in growing DNA strands?)

Answer 12

-The 3’OH is converted into an oxy anion that serves as a nucleophile to perform a nucleophilic attack on the alpha phosphate on the 5’ end of the incoming nucleotide. Results in phosphodiester bond formation.

Question 13

Define gene expression

Answer 13

-Gene expression=production of RNA (transcription)