Chapter 5b: The Central Dogma Revisit Flashcards
What term describes the process of DNA replication?
Semiconservative
What did Watson and Crick’s base pairing maintain during DNA replication?
Watson and Crick’s base pairing maintained the complementary base pairing between the nucleotides of the parent DNA strands and the newly synthesized strands.
In which direction does DNA synthesis occur?
5’ to 3’ direction
What is required for the initiation of DNA replication?
Primer
What is the term for the complex of enzymes and proteins involved in DNA replication?
Replisome
How does base pairing facilitate DNA replication?
Base pairing allows each strand of DNA to serve as a template for the synthesis of a new complementary strand.
What is another term for the copying of DNA?
DNA Replication
Who conducted the famous experiment supporting semi-conservative replication, and in what year was it conducted?
- Meselson and Stahl
- 1958
How did Meselson and Stahl label the parent and new nucleotides in their experiment?
- labeled the “parent” nucleotides in DNA strands with heavy nitrogen (15N)
- labeled the new nucleotides with a lighter isotope, nitrogen-14 (14N)
Explain the concept of semi-conservative replication as demonstrated by Meselson and Stahl.
- Semi-conservative replication means that each newly replicated DNA molecule consists of one parental strand (labeled with heavy nitrogen, 15N) and one newly synthesized strand (labeled with lighter nitrogen, 14N)
- Meselson and Stahl’s experiment confirmed this by showing that after one round of replication, DNA molecules appeared as hybrid “half-heavy” strands, supporting the semi-conservative model proposed by Watson and Crick.
What is the premise of the conservative model of DNA replication?
the parental double helix remains intact, and an entirely new copy is made.
What is the central idea behind the semiconservative model of DNA replication?
the two strands of the parental molecule separate, and each functions as a template for the synthesis of a new complementary strand.
What does the dispersive model propose regarding DNA replication?
each strand of both daughter molecules contains a mixture of old and newly synthesized parts.
What are replication bubbles?
regions of the DNA double helix where the two strands are separated, allowing for the replication machinery to access the template strands and synthesize new DNA strands.
What is a replication fork?
a structure that forms as the DNA strands are unwound during replication. It consists of two single-stranded DNA templates and serves as the site where DNA synthesis occurs.
How do replication forks move during DNA replication?
move bidirectionally away from the origin of replication as DNA replication proceeds.
What are the origins of replication in eukaryotic genomes?
Eukaryotic genomes typically contain multiple origins of replication to ensure efficient and timely replication of the entire genome.
What is the single origin of replication in prokaryotic genomes called?
oriC
What is the function of initiator proteins in prokaryotic DNA replication?
recognize the origin of replication (oriC) and initiate the assembly of the pre-replication complex.
What is the pre-replication complex (Pre-RC) in prokaryotic DNA replication?
a complex of proteins and enzymes assembled at the origin of replication (oriC), including proteins like DnaA, which play a crucial role in the initiation of DNA replication.
How are replication forks formed in prokaryotic DNA replication?
when the pre-replication complex assembles at the origin of replication (oriC), and the DNA helix is unwound.
Describe the process of bidirectional replication in prokaryotic DNA replication.
the growth of two replication forks outward from the origin of replication (oriC) in opposite directions. This means that DNA is unwound and new strands are synthesized simultaneously in both directions.
What role do DNA polymerases play in prokaryotic DNA replication?
At the replication forks, DNA polymerases and other enzymes synthesize new DNA strands complementary to the parental strands. DNA polymerases add nucleotides to the growing daughter strands in a 5’ to 3’ direction.
What is nucleotide incorporation?
a crucial step during DNA replication where new nucleotides are added to the growing DNA strand.
What are nucleoside triphosphates (dNTPs)? What does it consist of?
the building blocks used to synthesize DNA. Each consists of a nitrogenous base, a sugar (deoxyribose in DNA), and three phosphate groups.
What is the role of DNA polymerase in DNA replication? Where does it add nucleotides? What is its polymerization activity?
the enzyme responsible for catalyzing the addition of nucleotides to the growing DNA strand during replication. It adds nucleotides to the 3’ end of the growing DNA strand and has a 5’ to 3’ polymerization activity.
What is pyrophosphate (PPi) hydrolysis? What’s the byproduct? What is the product? What is it for?
occurs when a nucleotide is added to the growing DNA strand, releasing pyrophosphate as a byproduct. Pyrophosphate is hydrolyzed into two inorganic phosphate (Pi) molecules, providing the energy necessary for phosphodiester bond formation.
What is a nucleophilic attack? What is it in DNA replication? What does it produce?
a reaction mechanism where a nucleophile donates a pair of electrons to an electron-deficient atom or center, forming a new chemical bond. In DNA replication, it occurs during the formation of phosphodiester bonds between adjacent nucleotides.
The Different DNA Polymerases
DNA Polymerase I, II, and III
What are the 3 key characteristics of DNA polymerase I?
- 5’ to 3’ polymerization activity
- 3’ to 5’ proofreading activity
- 5’ to 3’ exonuclease activity for removing RNA primers during DNA replication.
What is the function of the 3’ to 5’ exonuclease domain in DNA polymerase I?
allows DNA polymerase I to proofread newly synthesized DNA by excising incorrectly added nucleotides from the 3’ end of the DNA strand.
What role does DNA polymerase II primarily play in DNA replication?
primarily functions in DNA repair processes, filling in gaps that arise during repair.
What is the primary function of DNA polymerase III?
the primary enzyme responsible for DNA replication in prokaryotes, such as bacteria. It synthesizes the majority of the new DNA strand during replication and has high processivity.
Characteristics of DNA Polymerases in E.coli:
What activity is present in DNA Polymerase I? (removes and replaces primers)
- 5’-3’ polymerase activity
- 3’-5’ exonuclease activity
- 5’-3’ exonuclease activity
Characteristics of DNA Polymerases in E.coli:
What activity is present in DNA Polymerase II? (DNA repair; restarts replication after damaged DNA halts synthesis)
- 5’-3’ polymerase activity
- 3’-5’ exonuclease activity
Characteristics of DNA Polymerases in E.coli:
What activity is present in DNA Polymerase III? (Elongates DNA)
- 5’-3’ polymerase activity
- 3’-5’ exonuclease activity
Characteristics of DNA Polymerases in E.coli:
What activity is present in DNA Polymerase IV? (DNA repair)
- 5’-3’ polymerase activity
Characteristics of DNA Polymerases in E.coli:
What activity is present in DNA Polymerase V? (DNA repair; translesion DNA synthesis)
- 5’-3’ polymerase activity
Proofreading during DNA replication
- Polymerase adds an incorrect nucleotide to the new strand.
- Polymerase detects that bases are mispaired.
- Polymerase uses 3’-5’ exonuclease activity to remove the incorrect nucleotide.
What is excision repair?
a DNA repair mechanism in which damaged DNA is recognized and removed, followed by the synthesis of a new DNA strand to fill in the gap.
The initial step in excision repair is the recognition of the damaged DNA, such as a __ __, which distorts the DNA molecule.
thymine dimer
Excision repair: A __ __ cuts the damaged DNA strand at two points, allowing the removal of the damaged section.
nuclease enzyme
Excision repair: Repair synthesis by a __ __ fills in the missing nucleotides using the __ __ __ as a template.
- DNA polymerase
- undamaged complementary strand
The final step of excision repair is __ __sealing the free end of the new DNA to the old DNA, completing the strand.
DNA ligase
The leading strand is synthesized continuously in the __ direction toward the __ __.
- 5’ to 3’
- replication fork
__ __ can synthesize the leading strand continuously because its orientation allows it to move in the __ direction as the replication fork’s progression.
- DNA polymerase
- same
The lagging strand is synthesized discontinuously in short fragments called __ __.
Okazaki fragments
__ __ synthesizes the lagging strand discontinuously because it moves in the __ direction of the replication fork’s movement, resulting in the need for discontinuous synthesis.
- DNA polymerase
- opposite
__ is an enzyme responsible for synthesizing RNA primers on the lagging strand, providing a starting point for __ __ to initiate the synthesis of each __ __.
- Primase
- DNA polymerase
- Okazaki fragment
__ enzymes are involved in relieving the tension that builds up ahead of the replication fork as DNA unwinds. They cut one or both strands of the DNA, allowing it to relax and prevent the formation of __.
- Topoisomerase
- supercoils
a protein that binds to the double helix ahead of the replication fork and relieves the strain placed on the double helix as it unravels.
topoisomerase
breaks the hydrogen bonds between the two strands. This allows the DNA to unwind into two strands at the replication fork.
DNA helicase
prevent the separated strands from joining together again by binding to the separated strands and stabilizing them.
Single-strand binding proteins (SSBs)
enzyme: initiation of replication
unwinding DNA?
providing single-stranded DNA templates?
- helicases
- single-strand binding proteins (SSBPs)
enzyme: synthesis of leading strand
priming?
elongation?
replacement of RNA primer by DNA?
- primase
- DNA polymerasae
- DNA polymerase
enzyme: synthesis of lagging strand
priming for okazaki fragment?
elongation of the fragment?
replacement of RNA primer by DNA?
joining of fragments?
- primase
- DNA polymerasae
- DNA polymerase
- ligase
Lagging-Strand Synthesis 1/2
(1) __ joins RNA nucleotides into a primer.
(2) __ __ __ adds DNA nucleotides to the primer, forming an __ __.
(3) After reaching the next __ __, __ __ __falls off.
- Primase
- DNA pol. III
- Okazaki fragment
- RNA primer
- DNA polymerase III
Lagging-Strand Synthesis 2/2
(4) After the second fragment is primed, __ __ __ adds DNA nucleotides until it reaches the first primer and falls off.
(5) __ __ __ replaces the RNA with DNA, adding to the 3’ end of the fragment 2.
(6) __ __ forms a bond between the newest DNA and the adjacent DNA of fragment 1.
(7) The lagging strand in this region is now complete.
- DNA polymerase III
- DNA polymerase I
- DNA ligase
__ is the process by which a segment of DNA is used as a template to synthesize a complementary RNA molecule.
- Transcription
The __ __ (__ __ __) in transcription is the DNA strand used as a template for RNA synthesis.
template strand (transcribed DNA strand)
The __ __ (__ __ __) is the DNA strand with the same sequence as the RNA molecule, except with thymine (T) replaced by uracil (U).
coding strand (non-transcribed DNA stand)
__ __ is the enzyme responsible for transcription.
RNA polymerase
Transcription: __ __ binds to the DNA template strand and synthesizes a complementary RNA strand in the __ direction.
- RNA polymerase
- 5’ to 3’
A __ __ is formed as RNA polymerase moves along the DNA template, unwinding the DNA double helix ahead of it to allow access to the template strand for RNA synthesis.
transcription bubble
a fundamental concept that describes the flow of genetic information within a biological system. Who proposed it?
- central dogma
- Francis Crick
- a specific DNA sequence where DNA replication begins.
- where the replication machinery binds and initiates the replication process.
- typically rich in adenine-thymine (AT) base pairs and have specific structural features that facilitate the binding of replication proteins.
Ori sequence
the building blocks used to synthesize DNA, consisting of a nitrogenous base, a sugar (deoxyribose in DNA), and three phosphate groups.
nucleoside triphosphates (dNTPs)
How does DNA polymerase add nucleotides?
DNA polymerase adds nucleotides to the 3’ end of the growing DNA strand in a 5’ to 3’ direction.
occurs when a nucleotide is added to the growing DNA strand, releasing PPi as a byproduct. This hydrolysis provides energy for bond formation.
Pyrophosphate (PPi) hydrolysis
the step where the 3’ hydroxyl group of the terminal nucleotide attacks the phosphate group of the incoming nucleotide triphosphate, forming a phosphodiester bond.
Nucleophilic attack
