Enzymes acting on nucleic acids #9

Question 1

what enzymes hydrolyze the ribose phosphate back bone? (the phosphodiester bond)

Answer 1

DNase, RNase. Exonucleases and Endonucleases

Question 2

what enzymes synthesize phosphodiester bonds

Answer 2

polymerase, ligase, transesterase (for RNA only)

Question 3

enzymes which modify DNA topology

Answer 3

topoisomerase, helicase

Question 4

enzymes modifying nucleic acid bases

Answer 4

transferring alkyl radicals, hydrolyzing the N-C glycosidic bond

Question 5

nucleases? What are the 2 kinds?

Answer 5

are enzymes which hydrolyze the phosphodiester bond.
~Endonucleases: they cleave within a polynucleotide chain
~Exonucleases: cleave at the end of a polypeptide chain

Question 6

specific endonucleases

Answer 6

~Type 1: cut DNA at random locations 1000 bp from the recognition site
~Type 2: cut DNA within their recognized sequence. These are normally 4-6 bp, and are palindromic
~Type 3: recognize a symmetric sequence, but cut DNA outside the recognition site (20-30bp after)

Question 7

restriction is the combined activity of?

Answer 7

a methylase and an endonuclease. This is used by bacteria to prevent infections.
Class 2 restriction enzymes are just endonucleases
class 1+3 are endonucleases and methylases

Question 8

methylated sequences are recognized as?

Answer 8

self molecules

Question 9

the formula between sequence length and recurrence frequency

Answer 9

recurrence frequency = 4^sequence length. Meaning a sequence of N nucleotides occurs on an average of 4^N nucleotides

Question 10

sickle cell RBC have what aa instead of GLU

Answer 10

VAL

Question 11

DNA polymerase

Answer 11

catalyzes the addition of a deoxyribonucleotide to the 3’-OH end of a polynucleotide chain(the primer strand)

Question 12

the activities of reverse transcriptase enzymes?

Answer 12

~DNA polymerase activity: it synthesizes a DNA copy of an RNA molecule
~RNase H activity: degrades RNA in RNA-DNA hybrids

Question 13

where is reverse transcriptase present in a eukaryotic cell?

Answer 13

~retroviruses
~endogenous viruses
~retrotransposons
~in telomerase

Question 14

DNA ligase function

Answer 14

the formations of a phosphodiester bond between a 3’-OH group and a 5’ phosphate group
(adenylation, transfer of AMP to 5’ phosphate, formation of the ppd bond)

Question 15

what is the chemical sequencing of Maxam and Gilbert

Answer 15

when DNA is subjected to controlled chemical treatments that generate breaks of the molecules at specific nucleotides

Question 16

what is the enzymatic sequencing of Sanger

Answer 16

DNA is sequenced by polymerization in the presence of dideoxynucleotide triphosphates ddNTP’s as DNA chain terminators. The sequence is read form the bottom to the top and gives the reading of the complementary sequence of the DNA strand