DNA Replication during the S Phase Flashcards
The general pathway for the flow of genetic
information, known as the Blank of
molecular biology
“Central Dogma”
Central Dogma is proposed by
Francis Crick
is the long-term storage molecule of the
hereditary information that determines the
development, structure, function, and reproduction of
an organism.
DNA
two classes of macromolecules are among the major
players in molecular biology.
- The proteins and nucleic acids.
DNA replication is ?
semi-conservative.
What does semi-conservative mean?
each strand might serve as a
template for the formation of a complementary
daughter strand.
The enzymatic synthesis of DNA
requires two essential
substrates:
- the four deoxynucleoside
triphosphates (dNTPs) - and a primer
What are the four deoxynucleoside
triphosphates (dNTPs) ?
dATP, dGTP, dCTP, dTTP,
What is the primer?
template junction.
Where does the three phosphoryl groups attached?
2’ deoxyribose via the 5’- hydroxyl.
The deoxynucleoside
triphosphates have three
phosphoryl groups
α = proximal position, β= middle position, γ =
distal position
are high energy bonds.
The β and γbonds
The primer: template junction
has two essential components.
single-stranded DNA template, short primer
First is the Blank that will direct the
addition of the complementary
deoxynucleotides in the growing
chain.
single-stranded DNA template
second is the Blank
that is also complementary to
the template. This primer is
consists of RNA and not DNA
short primer
Since the two strands of a double -
stranded DNA molecule have an
antiparallel orientation, the
template strand must have an
orientation Blank that is opposite
to that of the growing DNA strand.
(3’ → 5’)
During the synthesis the
phosphodiester bond is formed
in an Blank
SN2 reaction.
The leaving group in the
reaction is Blank
pyrophosphate
ΔG of this reaction is rather small (ΔG=
3.5 kcal/mol) but additional free energy is
provided by the hydrolysis of the
pyrophosphate by the enzyme
Blank.
pyrophosphatase.
Whole synthesis is a coupled process
driven by the Blank.
hydrolysis of pyrophosphate
is an unusual enzyme because it uses a single active site to catalyze the addition of any of four dNTPs
DNA polymerase (and also RNA polymerase)
This discrimination is mediated by the Blank from the active site.
steric exclusion of the rNTPs
This space is occupied by two amino acids, the Blank of the active site that make van der Waals contacts with the sugar ring.
the discriminator amino acids
The palm domain provides the Blank due to the important conserved sequence motifs that it contains.
catalytic active site
The Blank help in positioning the template the active site
correctly. It also associates with the template.
fingers
One of the helices of the finger domain, called the Blank
rotates by 40° when the correct base pair has been formed.
O-helix
The Blank is not directly involved in catalysis.
interacts with the DNA that has been most recently
synthesized and leaves the enzyme.
thumb domain
In other words, the DNA polymerase is a Blank.
processive enzyme
depends on the interactions of
the minor groove of the DNA and the palm
domain (H-bonds), the electrostatic
interactions with the thumb domain, and is
further increased through interactions
between the polymerase and a Blank
protein that completely encircles the DNA.
Processivity
“sliding clamp”
- the junction between the newly synthesized DNA and the unreplicated duplex
- moves continuously thereby generating two single-stranded templates that direct the formation of two
daughter DNA duplexes
Replication fork
Demonstrates the coordinated synthesis of leading and lagging strand DNA by the replisome
Trombone Model
is composed of
several identical subunits assembled
in a doughnut-like structure, with a
central hole (about 35 Å) that is large
enough to encircle the dsDNA (20 Å)
and leaves space for 1 or 2 layers of
H2O molecules.
The sliding clamp
The clamp structure is loaded onto the
DNA by the Blank
sliding clamp loader
Catalyzes the opening of the sliding clamp structure and place it on DNA at
the primer:template junction,
* requires ATP-binding to the clamp loader
Sliding clamp loader
For coordination of leading and lagging strand synthesis
DNA Pol III Holoenzyme
protects the telomeric ends of chromosomes
The telomere cap structure
- form a looped structure (t-loop)
that protects chromosome ends - protects chromosome
- avoid engaging in DNA repair like
dsDNA breaks
Telomeres
