Chapter 4A: Enzymes that manipulate DNA

Question 1

Endonuclease

Answer 1

an enzyme that breaks the phosphodiester bond between two nucleotides in a polynucleotide chain

- They target specific recognition sites
- Known as 'molecular scissors'
- Either create sticky or blunt ends
- its substrates are the nitrogenous bases

Question 2

Restriction Endonuclease

Answer 2

any enzyme that acts like a molecular scissor to cut nucleic acid strands at specific recognition sites.

- Aka restriction enzyme

Question 3

Recognition Site

Answer 3

a specific base sequence of DNA which restriction endonucleases act upon

- Usually 4-6 nucleotides in length 
- Usually palindromes(5'-3' sequence is identical on both strands)

Question 4

Sticky End

Answer 4

the result of a staggered cut through double stranded DNA by an endonuclease resulting in overhanging nucleotides

- E.g. Recognition sequence for EcoRI
- Overhanging nucleotides will want to stick to a complementary set of unpaired nucleotides

Question 5

Blunt End

Answer 5

the result of a straight cut across double stranded DNA by an endonuclease resulting in no overhanging nucleotides

- E.g. Recognition sequence for Alul

Question 6

Ligase

Answer 6

an enzyme that joins molecules, including DNA or RNA together by catalyzing the formation of phosphodiester bonds

- Acts like 'molecule glue'
- Lack specificity meaning they can join any blunt or sticky end. 
- The substrates are the sugar and phosphate groups

Question 7

Phosphodiester bond

Answer 7

a strong covalently linked bond between a 5 carbon sugar and a phosphate group in a nucleic acid chain

Question 8

Types of Ligase Enzymes

Answer 8

• DNA ligase: joins DNA fragments(okazaki fragments)

- RNA ligase: joins RNA fragments

Question 9

Polymerase

Answer 9

an enzyme that synthesises a polymer from monomers

- E.g. Forming DNA from nucleotides
- Require a primer to attach to the start of the template strand
- Read and synthesises a complementary strand in a 5' to 3' direction

Question 10

Types of Polymerase

Answer 10

RNA Polymerase:
- primarily used in the transcription of genes

DNA Polymerase:

- is used in the replication or amplification of DNA 
    - Synthesises DNA in a 5' to 3' direction

Question 11

Primer

Answer 11

a short, single strand of nucleic acids that act as a starting point for polymerase enzymes to attach

Question 12

Types of Primers

Answer 12

• Forward Primers

- Reverse Primers

Question 13

Forward Primer

Answer 13

Forward Primer: Binds to start codon at the 3’ end of template strand

- Causes Taq polymerase to synthesise a new DNA strand in the direction RNA polymerase would function

Question 14

Reverse Primer

Answer 14

Reverse Primer: binds at the stop codon at the 3’ end of the coding strand

- Causes Taq polymerase to synthesize a new DNA strand in the opposite direction to which RNA polymerase would function