DNA Replication during the S Phase

Question 1

The general pathway for the flow of genetic
information, known as the Blank of
molecular biology

Answer 1

“Central Dogma”

Question 2

Central Dogma is proposed by

Answer 2

Francis Crick

Question 3

is the long-term storage molecule of the
hereditary information that determines the
development, structure, function, and reproduction of
an organism.

Answer 3

DNA

Question 4

two classes of macromolecules are among the major
players in molecular biology.

Answer 4

• The proteins and nucleic acids.

Question 5

DNA replication is ?

Answer 5

semi-conservative.

Question 6

What does semi-conservative mean?

Answer 6

each strand might serve as a
template for the formation of a complementary
daughter strand.

Question 7

The enzymatic synthesis of DNA
requires two essential
substrates:

Answer 7

• the four deoxynucleoside
  triphosphates (dNTPs)
• and a primer

Question 8

What are the four deoxynucleoside
triphosphates (dNTPs) ?

Answer 8

dATP, dGTP, dCTP, dTTP,

Question 9

What is the primer?

Answer 9

template junction.

Question 10

Where does the three phosphoryl groups attached?

Answer 10

2’ deoxyribose via the 5’- hydroxyl.

Question 10

The deoxynucleoside
triphosphates have three
phosphoryl groups

Answer 10

α = proximal position, β= middle position, γ =
distal position

Question 11

are high energy bonds.

Answer 11

The β and γbonds

Question 12

The primer: template junction
has two essential components.

Answer 12

single-stranded DNA template, short primer

Question 13

First is the Blank that will direct the
addition of the complementary
deoxynucleotides in the growing
chain.

Answer 13

single-stranded DNA template

Question 14

second is the Blank
that is also complementary to
the template. This primer is
consists of RNA and not DNA

Answer 14

short primer

Question 15

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.

Answer 15

(3’ → 5’)

Question 16

During the synthesis the
phosphodiester bond is formed
in an Blank

Answer 16

SN2 reaction.

Question 17

The leaving group in the
reaction is Blank

Answer 17

pyrophosphate

Question 18

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.

Answer 18

pyrophosphatase.

Question 19

Whole synthesis is a coupled process
driven by the Blank.

Answer 19

hydrolysis of pyrophosphate

Question 20

is an unusual enzyme because it uses a single active site to catalyze the addition of any of four dNTPs

Answer 20

DNA polymerase (and also RNA polymerase)

Question 21

This discrimination is mediated by the Blank from the active site.

Answer 21

steric exclusion of the rNTPs

Question 22

This space is occupied by two amino acids, the Blank of the active site that make van der Waals contacts with the sugar ring.

Answer 22

the discriminator amino acids

Question 22

The palm domain provides the Blank due to the important conserved sequence motifs that it contains.

Answer 22

catalytic active site

Question 23

The Blank help in positioning the template the active site
correctly. It also associates with the template.

Answer 23

fingers

Question 23

One of the helices of the finger domain, called the Blank
rotates by 40° when the correct base pair has been formed.

Answer 23

O-helix

Question 24

The Blank is not directly involved in catalysis.
interacts with the DNA that has been most recently
synthesized and leaves the enzyme.

Answer 24

thumb domain

Question 25

In other words, the DNA polymerase is a Blank.

Answer 25

processive enzyme

Question 26

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.

Answer 26

Processivity

“sliding clamp”

Question 27

• 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

Answer 27

Replication fork

Question 28

Demonstrates the coordinated synthesis of leading and lagging strand DNA by the replisome

Answer 28

Trombone Model

Question 29

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.

Answer 29

The sliding clamp

Question 30

The clamp structure is loaded onto the
DNA by the Blank

Answer 30

sliding clamp loader

Question 31

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

Answer 31

Sliding clamp loader

Question 32

For coordination of leading and lagging strand synthesis

Answer 32

DNA Pol III Holoenzyme

Question 33

protects the telomeric ends of chromosomes

Answer 33

The telomere cap structure

Question 34

• form a looped structure (t-loop)
  that protects chromosome ends
• protects chromosome
• avoid engaging in DNA repair like
  dsDNA breaks

Answer 34

Telomeres