DNA Replication Flashcards
Mismatch Repair System
corrects mistakes made by (my) DNA Polymerase
What is the purpose of DNA replication?
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).
What happens immediately after replication?
DNA is hemimethylated
hemimethylated
the old strand still has methyl groups attached to various bases, but the new strand has not been methylated yet
replication fork
Region where the enzymes replicating a DNA molecule are bound to untwisted, single-stranded DNA (Y-shaped)
DNA adenine methylase
adds a methyl group to the adenine in GATC
origin of replication (ori)
Site on a chromosome or any other DNA molecule where replication begins
has mostly AT base pairs
DNA cytosine methylase
adds a methyl group to the cytosine in CCAGG or CCTGG
replisome
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
What are the breaks along the lagging strand called?
nicks
leading strand
The new strand of DNA that is synthesized continuously during replication - there is always a free 3 -OH group.
What does DNA Polymerase 1 do?
removes RNA primers from the lagging strand
lagging strand
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.
RNaseH
an enzyme that specifically identifies RNA:DNA hetero-duplexes and removes the RNA bases
How are the DNA fragments of the lagging strand linked?
DNA ligase (through a ligation reaction)
DNA Ligase
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
What is the last step of DNA Replication?
Methyl (CH3) groups are added along the new strand.
DNA polymerase 3
the major form of DNA polymerase used to replicate bacterial chromosomes and consists of multiple protein subunits
semiconservative replication
Mode of DNA replication in which each daughter molecule gets one of the two original strands and one new complementary strand
sliding clamp
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.
DNA helicase
Enzyme that unwinds double-helical DNA by dissolving the hydrogen bonds between paired bases
DNA gyrase
removes supercoiling
An enzyme that introduces negative supercoils into DNA, a member of the type II topoisomerase family
What are the three subunits of core enzymes
DnaE (alpha subunit), DnaQ (sigma subunits), HolE (theta subunit)
DnaE (alpha subunits)
links the nucleotides together
single-stranded binding protein
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
DnaQ (sigma subunits)
proofreads the new strand
catenated
Structure in which two or more circles of DNA are interlocked
HolE (theta subunits)
stabilizes the two other subunits (DnaE and DnaQ)
Replication of Circular Chromosomes
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.
Why can DNA polymerase not initiate new strands of nucleic acid synthesis
because they can only add a nucleotide onto a pre-existing 3’-OH
