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Genetics summary chapter 11 VU amsterdam
- Instelling
- Vrije Universiteit Amsterdam (VU)
This summary covers complete chaper 11 of genetics at the Vrije Universiteit Amsterdam.
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Chapter 11 summary- DNA replication: copying the genetic material in order to pass it from parent to offspring.
The original DNA strands are used as the templates (parental strands) for the synthesis of new DNA
strands. After the double helix has separated, individual nucleotides have access to the template
strands. To complete the replication process, a covalent bond is formed between the phosphate of
one nucleotide and the sugar molecule of the other nucleotide. The two newly made strands are
called the daughter strands.
Scientists in the late 1950s considered 3 different mechanisms to explain the end result of DNA
replication: Meselson and Stahl.
1. Conservative model: both parental strands of the DNA remain together following DNA
replication. In this model, the original arrangement of parental strands is completely
conserved, and the two newly made daughter strands also remain together following
replication.
2. Semiconservative model: the double-stranded DNA is half conserved following the
replication process. The newly made double-stranded DNA contains one parental strand and
one daughter strand.
3. Dispersive model: segments of the parental DNA and newly made DNA are interspersed in
both strands following the replication process.
By labelling DNA with heavy and light isotopes of nitrogen and using centrifugation, Meselson and
Stahl showed that DNA replication is semiconservative.
Bacterial DNA replication
The site on the bacterial chromosome where DNA synthesis begins is known as the origin of
replication (single). The synthesis of new daughter strands it initiated within the origin and proceeds
in both directions, bidirectionality, around the bacterial chromosome. This means that two
replication forks, the region where the parental strands have separated and new daughter strands
are being made, move in opposite directions outward from the origin. Eventually, the replication
forks meet each other on the opposite side of the bacterial chromosome.
Replication is initiated by the binding of DnaA proteins to the origin of replication. DNA replication
begins with the binding of DnaA proteins to sequences within the origin of replication known as the
DnaA boxes. When DnaA proteins are in their ATP-bound form, they bind to five DnaA boxes to
initiate DNA replication. DnaA proteins also bind to each other to form a complex. Other DnaA
proteins such as HU and IHF cause the DNA to bend around the complex of DnaA proteins, which
results in the separation of the strands at the AT-rich region. Because only 2 hydrogen bonds form
between AT and 3 between CG, the DNA strands are more easily separated at an AT-region.
Following the separation at the AT-region, the DnaA proteins with the help of DnaC proteins, attract
DNA helicase to this site. When a DNA helicase encounters a double-stranded region, it breaks the
hydrogen bonds between the two strands, thereby generating two single strands. Two DNA helicases
begin strand separation with the origin of replication and continue to separate the DNA strands
beyond the origin. These proteins use their energy from ATP hydrolysis to catalyse the separation. In
E.coli, DNA helicases bind to a single-stranded DNA and travel along the DNA in an 5’->3’ direction to
keep the replication fork moving. The action of DNA helicases promotes the movement of replication
forks. This initiates the replication of the bacterial chromosome in both directions termed
bidirectional replication.
The GATC methylation sites within the origin of replication are involved with regulating the DNA
replication. These sites are methylated by an enzyme known as (DNA adenine methyltransferase)
Dam. Prior to DNA replication, the GATC sites are methylated in both strands. This full methylation
makes the initiation of DNA replication at the origin of replication easier. Following the DNA
, Chapter 11 summary
replication, the newly made strands are not methylated, because adenine rather than methyladenine
is incorporated into the daughter strands. So first the methylation, then the DnaA proteins.
1. Unwinding the double helix
The function of DNA helicase is to break the hydrogen bonds between base pairs and thereby
unwind the strand; this action generates positive supercoiling ahead of each replication fork.
An enzyme known as topoisomerase II (DNA gyrase) travels in front of the DNA helicase and
alleviates positive supercoiling. After the parental DNA strands have been separated and the
positive supercoiling is relaxed, the strands must be kept this way until the complementary
daughter strands have been made. Single-strand binding proteins, which bind to the strands
of parental DNA, prevent them from re-forming a double helix. In this way, the bases within
parental strands are kept in an exposed condition that allows them to hydrogen bond with
individual nucleotides.
2. Synthesis of RNA primers via primase
The next event in DNA replication is the synthesis of short strands of RNA called RNA
primers. These strands of RNA are synthesized by the linkage of ribonucleotides via an
enzyme called primase. Primase synthesizes short strands of RNA, these short RNA strands
start the DNA replication. In the leading strand, a single primer is made at the origin of
replication. In the lagging strand, multiple primers are made. The RNA primers are eventually
removed.
3. Synthesis of DNA via DNA polymerase
An enzyme known as DNA polymerase is responsible for synthesizing the DNA along the
leading and lagging strands. This enzyme catalyzes the formation of covalent bonds between
the nucleotides, thereby producing a new daughter strand. DNA polymerase I and III are
involved in normal DNA replication, whereas DNA polymerase II is involved in the replication
of damaged DNA. DNA polymerase III is responsible for synthesizing the daughter strand. It is
a large enzyme consisting of 10 different sub-units that play various roles in the DNA
replication process. The α subunit catalyzes the bond formation between the nucleotides,
and the remaining 9 subunits fulfil other functions. The complex of all 10 subunits together is
called DNA polymerase III holoenzyme.
DNA polymerase I is composed of one subunit. Its role is to remove the RNA primers and fills
in with DNA. The catalytic subunit of all the DNA polymerases has a structure of a human
hand. The incoming deoxyribonucleoside triphosphates (dNTPs) enter the catalytic site, bind
to the template strand and then are covalently attached to the 3’ exonuclease site that
removes mismatched bases.
DNA polymerase cannot begin DNA synthesis by linking together the first two individual
nucleotides. Rather, this type of enzyme can only elongate a strand starting with an RNA
primer or an existing DNA strand. A second unusual feature is the directionality of the strand
synthesis. DNA polymerase can only attach nucleotides from the 5’ -> 3’ direction.
The leading strand, the DNA synthesis is made continuously. However, in the lagging strand, this is
not the case, because it runs from 3’ -> 5’ and DNA replication can only go from 5’ -> 3’. Therefore,
the DNA polymerase can make this strand in small chunks called Okazaki fragments. Each fragment
is started with a RNA primer (made by primase, which ads a few RNA nucleotides that form the RNA
primer). DNA polymerase III than adds a short row of DNA bases in the 5’ -> 3’ direction. The next
RNA primer is than added further down the lagging strand. Another Okazaki fragment is then made
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