DNA Replication

Question 1

Mismatch Repair System

Answer 1

corrects mistakes made by (my) DNA Polymerase

Question 2

What is the purpose of DNA replication?

Answer 2

Replication copies the entire set of genomic DNA so that the cell can divide in two.

DNA unwinds and the hydrogen bonds melt apart to form two single strands.

Happens much faster in bacteria (1000 nucleotides/second) than in eukaryotes (50 nucleotides/second).

Question 3

What happens immediately after replication?

Answer 3

DNA is hemimethylated

Question 4

hemimethylated

Answer 4

the old strand still has methyl groups attached to various bases, but the new strand has not been methylated yet

Question 5

replication fork

Answer 5

Region where the enzymes replicating a DNA molecule are bound to untwisted, single-stranded DNA (Y-shaped)

Question 6

DNA adenine methylase

Answer 6

adds a methyl group to the adenine in GATC

Question 7

origin of replication (ori)

Answer 7

Site on a chromosome or any other DNA molecule where replication begins

has mostly AT base pairs

Question 8

DNA cytosine methylase

Answer 8

adds a methyl group to the cytosine in CCAGG or CCTGG

Question 9

replisome

Answer 9

synthesizes the complementary strand on one side of the fork by adding complementary bases in a 5’ to 3’ direction

Assemblage of proteins (including primase, DNA polymerase, helicase, SSB protein) that replicates DNA

Question 10

What are the breaks along the lagging strand called?

Answer 10

nicks

Question 10

leading strand

Answer 10

The new strand of DNA that is synthesized continuously during replication - there is always a free 3 -OH group.

Question 11

What does DNA Polymerase 1 do?

Answer 11

removes RNA primers from the lagging strand

Question 12

lagging strand

Answer 12

The new strand of DNA that is synthesized in short pieces (okazaki fragments) during replication and then joined later

clamp loader is continuously released and reattached at a new location -> results in a single-stranded region bubbling out from the repliosome.

Question 13

RNaseH

Answer 13

an enzyme that specifically identifies RNA:DNA hetero-duplexes and removes the RNA bases

Question 14

How are the DNA fragments of the lagging strand linked?

Answer 14

DNA ligase (through a ligation reaction)

Question 15

DNA Ligase

Answer 15

Enzyme that joins DNA fragments covalently, end to end

links 3 -OH and 5 PO4 of neighboring nucleotides to form phosphodiester bond

seals nicks in the backbone using ATP

Question 16

What is the last step of DNA Replication?

Answer 16

Methyl (CH3) groups are added along the new strand.

Question 17

DNA polymerase 3

Answer 17

the major form of DNA polymerase used to replicate bacterial chromosomes and consists of multiple protein subunits

Question 18

semiconservative replication

Answer 18

Mode of DNA replication in which each daughter molecule gets one of the two original strands and one new complementary strand

Question 19

sliding clamp

Answer 19

donut shaped protein consisting of a dimer of DnaN proteins (also called beta subunits)

binds DNA polymerase to the DNA template and prevents this enzyme from dissociating from the template DNA strand.

Question 20

DNA helicase

Answer 20

Enzyme that unwinds double-helical DNA by dissolving the hydrogen bonds between paired bases

Question 21

DNA gyrase

Answer 21

removes supercoiling

An enzyme that introduces negative supercoils into DNA, a member of the type II topoisomerase family

Question 22

What are the three subunits of core enzymes

Answer 22

DnaE (alpha subunit), DnaQ (sigma subunits), HolE (theta subunit)

Question 23

DnaE (alpha subunits)

Answer 23

links the nucleotides together

Question 24

single-stranded binding protein

Answer 24

A protein that keeps separated strands of DNA apart by coating the single stranded regions - allows the other enzymes to gain access to the origin and begin replication

Question 25

DnaQ (sigma subunits)

Answer 25

proofreads the new strand

Question 26

catenated

Answer 26

Structure in which two or more circles of DNA are interlocked

Question 27

HolE (theta subunits)

Answer 27

stabilizes the two other subunits (DnaE and DnaQ)

Question 28

Replication of Circular Chromosomes

Answer 28

Circular Chromosomes may be catenated together but topoisomerase IV releases the catenated daughter strands by introducing double-stranded nicks into one chromosome. The second copy than passes through the first which creates two separate molecules.

Question 29

Why can DNA polymerase not initiate new strands of nucleic acid synthesis

Answer 29

because they can only add a nucleotide onto a pre-existing 3’-OH