RE Basics
What is another name for a restriction enzyme?
(MYSTERY points: 200)
Restriction endonuclease
(MYSTERY points: 200)
EcoRI recognizes the sequence GAATTC. What special pattern does this recognition site have, and how do you identify it on both DNA strands?(MYSTERY points: 400)
It is a palindromic sequence. When both complementary strands are read in the 5′ → 3′ direction, they read the same sequence.
(MYSTERY points: 400)
EcoRI and SmaI both cut double-stranded DNA. Which one produces sticky ends, which one produces blunt ends, and what causes the difference? (MYSTERY points: 500)
EcoRI produces sticky ends because it makes staggered cuts.
SmaI produces blunt ends because it cuts both strands at the same position.
(MYSTERY points: 500)
Which restriction enzyme type is most commonly used in biotechnology?
(MYSTERY points: 200)
Type II
(MYSTERY points: 200)
A scientist cuts a gene of interest and a plasmid with compatible restriction enzymes. The DNA fragments pair, and another enzyme seals the backbone. What biotechnology application is this, and what enzyme seals the DNA? (MYSTERY points: 500)
Gene cloning / recombinant DNA technology, and DNA ligase seals the DNA backbone.
(MYSTERY points: 500)
Why are restriction enzymes called "molecular scissors"?
Because they cut DNA at specific sequences.
What recognition sequence does EcoRI recognize?
GAATTC
A restriction enzyme makes a staggered cut. What type of ends are produced?
Sticky ends
Where do Type II restriction enzymes usually cut DNA?
At or very near the recognition site.
What enzyme joins DNA fragments together after restriction enzymes cut them?
DNA ligase
What type of virus do restriction enzymes help bacteria defend against?
Bacteriophages
What special type of sequence is GAATTC?
A palindromic sequence
What is the single-stranded region sticking out from a sticky end called?
An overhang
Why are Type II restriction enzymes useful in biotechnology?
They make predictable cuts / produce predictable DNA fragments.
Which technique separates DNA fragments to produce band patterns?
Gel electrophoresis
What enzyme adds methyl groups to bacterial DNA to help protect it from being cut?
Methylase
In a DNA palindrome, in what direction must both strands be read?
5′ → 3′
Why can two compatible sticky ends attach to each other?
Their complementary bases can base-pair.
Can Type II restriction enzymes produce only sticky ends?
No. They can produce sticky or blunt ends.
In forensic science, DNA band patterns from a crime scene may be compared with DNA from whom?
Suspects
What bonds in the DNA backbone are broken by restriction enzymes?
Phosphodiester bonds
EcoRI is looking at this DNA:
5′–CTAGAATTCCG–3′
Which six bases make up its recognition site?
GAATTC
EcoRI cuts:
5′–G|AATTC–3′
3′–CTTAA|G–5′
What is the sticky-end overhang?
AATT
In the name EcoRI, what does the Roman numeral I mean?
It was the first restriction enzyme identified from that bacterial strain.
Which application uses known restriction sites and DNA fragment sizes to determine the arrangement of sites on DNA?
Restriction mapping