Transcript Chapter 10 - Evangel University
Mary K. Campbell Shawn O. Farrell http://academic.cengage.com/chemistry/campbell
Chapter Ten Biosynthesis of Nucleic Acids: Replication
Paul D. Adams • University of Arkansas
Replication of DNA
• Naturally occurring DNA exists in single-stranded and double-stranded forms, both of which can exist in ________ and ________ forms • Difficult to generalize about all cases of DNA replication • We will study the replication of ________ ________ ________ DNA and then of ________ ________ ________ DNA • most of the details we discuss were first investigated in ________, particularly ________ ________
Flow of Genetic Information in the Cell
• Mechanisms by which information is transferred in the cell is based on the “________ ________”
Prokaryotic Replication
• Challenges in duplication of ________________ double-stranded DNA • achievement of continuous ________ and separation of the two DNA strands • ________ of ________ portions from attack by ________ that attack single-stranded DNA • synthesis of the DNA ________ from one 5’ -> 3’ strand and one 3’ -> 5’ strand • efficient protection from ________ in replication
Prokaryotic Replication (Cont’d)
• • Replication involves ________ of the two original strands and ________ of two new daughter strands using the ________ strands as ________
_________________ replication:
each daughter strand contains one template strand and one newly synthesized strand • Incorporation of isotopic label as sole _________ source ( 15 NH 4 Cl) • Observed that 15 N-DNA has a higher density than 14 N-DNA, and the two can be separated by density-gradient ______________
Which Direction does Replication go?
• DNA double helix unwinds at a specific point called an ______________________________ • Polynucleotide chains are synthesized in both directions from the origin of replication; DNA replication is _______________ in most organisms • At each origin of replication, there are two _________ _____________, points at which new polynucleotide chains are formed • There is ______ origin of replication and ________ replication forks in the circular DNA of prokaryotes • In replication of a _______________ chromosome, there are several origins of replication and two replication forks at each origin
DNA Polymerase
• DNA is synthesized from its 5’ -> 3’ end (from the 3’ -> 5’ direction of the template) • the ________
strand
is synthesized continuously in the 5’ -> 3’ direction toward the replication fork • the ________
strand
(________ fragments) is synthesized __________ also in the 5’ -> 3’ direction, but away from the replication fork • lagging strand fragments are joined by the enzyme
DNA
___________
DNA Polymerase
DNA Polymerase Reaction
• The 3’-OH group at the end of the growing DNA chain acts as a _______________.
• The ______________ adjacent to the sugar is attacked, and then added to the growing chain.
Properties of DNA Polymerases
• There are at least _______ types of
DNA polymerase
(Pol) in
E coli
, _______ of which have been studied extensively
Function of DNA Polymerase
• DNA polymerase function has these requirements: • all four deoxyribonucleoside triphosphates: dTTP, dATP, dGTP, and dCTP • Mg 2+ • an _________ - a short strand of RNA to which the growing polynucleotide chain is covalently bonded in the early stages of replication • DNA-Pol I: repair and patching of DNA • DNA-Pol III: responsible for the polymerization of the newly formed DNA strand • DNA-Pol II, IV, and V: proofreading & repair enzymes
Supercoiling and Replication
•
DNA
_________ (class II topoisomerase) catalyzes rxn involving relaxed circular DNA: • creates a _______ in relaxed circular DNA • a slight unwinding at the point of the nick introduces _______ • the nick is _______ • The energy required for this process is supplied by ____________________
Replication with Supercoiled DNA
• Replication of supercoiled circular DNA •
DNA gyrase
has different role here. It introduces a nick in supercoiled DNA • • a _______ point is created at the site of the _______ • the gyrase opens and _______ the swivel point in advance of the replication fork • the newly synthesized DNA automatically assumes the ___________ form because it does not have the nick at the swivel point • _______ , a helix-destabilizing protein, promotes unwinding by binding at the replication fork
single-stranded binding (SSB) protein
_______ single-stranded regions by _______ tightly to them
Primase Reaction
• The primase reaction • RNA serves as a _______ in DNA replication • • _______ activity first observed
in-vivo
.
Primase -
catalyzes the copying of a short stretch of the DNA template strand to produce RNA primer sequence • __________ and _________ of new DNA strands • begun by DNA polymerase III • the newly formed DNA is linked to the 3’-OH of the RNA primer • as the replication fork moves away, the RNA primer is removed by DNA polymerase I
Replication Fork General Features
DNA Replication in Prokaryotes
• DNA synthesis is bidirectional • DNA synthesis is in the 5’ -> 3’ direction • the leading strand is formed continuously • the lagging strand is formed as a series of Okazaki fragments which are later joined • Five DNA polymerases have been found to exist in
E. coli
• Pol I is involved in synthesis and repair • Pol II, IV, and V are for repair under unique conditions • Pol III is primarily responsible for new synthesis
DNA Replication in Prokaryotes
• Unwinding • DNA gyrase introduces a swivel point in advance of the replication fork • a helicase binds at the replication fork and promotes unwinding • single-stranded binding (SSB) protein protects exposed regions of single-stranded DNA • Primase catalyzes the synthesis of RNA primer • Synthesis • catalyzed by Pol III • primer removed by Pol I • DNA ligase seals remaining nicks
Proofreading and Repair
• DNA replication takes place only once each generation in each cell • Errors in replication (
mutations
) occur spontaneously only once in every 10 9 to 10 10 base pairs • • Can be lethal to organisms
Proofreading
- the removal of incorrect nucleotides immediately after they are added to the growing DNA during replication (
Figure 10.10
) • Errors in hydrogen bonding lead to errors in a growing DNA chain once in every 10 4 to 10 5 base pairs
Proofreading Improves Replication Fidelity
• ____________________: catalyzed by Pol I: cutting is removal of the RNA primer and patching is incorporation of the required deoxynucleotides • ______________________
:
Pol I removes RNA primer or DNA mistakes as it moves along the DNA and then fills in behind it with its polymerase activity • ______________________
:
enzymes recognize that two bases are incorrectly paired, the area of mismatch is removed, and the area replicated again • ______________________
:
a damaged base is removed by DNA glycosylase leaving an AP site; the sugar and phosphate are removed along with several more bases, and then Pol I fills the gap
DNA Polymerase Repair
Mismatch Repair in Prokaryotes
• Mechanisms of mismatch repair encompass:
Eukaryotic Replication
• Not as understood as prokaryotic. Due in part to higher level of complexity.
• Cell growth and division divided into phases: M, G 1 , S, and G 2
Eukaryotic Replication
• Best understood model for control of eukaryotic replication is from yeast.
• DNA replication initiated by chromosomes that have reached the G 1 phase
Eukaryotic DNA Polymerase
• At least 15 different polymerases are present in eukaryotes (5 have been studied more extensively)
Structure of the PCNA Homotrimer
• PCNA is the eukaryotic equivalent of the part of Pol III that functions as a sliding clamp ( ).
The Eukaryotic Replication Fork
The general features of DNA replication in eukaryotes are similar to those in prokaryotes. Differences summarized in Table 10.5.
Telomerase and Cancer
(Biochemical Connections)
• Replication of linear DNA molecules poses particular problems at __________________ of the molecules • Ends of eukaryotic chromosomes called ______________________
:
__________________________________________ • See figures on p. 282-283