Flashcards in Chapter 6 and 7 Deck (63)
What is the unit of DNA replication
In prokaryotic and plasmid genomes, there is/are typically ____ origin(s) of replications
T/F DNA synthesis can be initiated without a template
false. DNA synthesis cannot be initiated, the nucleotides can only be added to an existing partially double stranded poly nucleotide sequence.
New nucleotides are added to the ____ end of the strand
What kind of model did Meselson and Stahl propose for DNA replication? How did they achieve this?
They proposed the semi-conservative model, used 5-bromodeoxyuridine that replaced thiamine bases, and after two rounds of DNA replication, the sister chromatids had different chemical content, indicating that they were attached to an old strand.
They used equilibrium density gradient centrifugation that allowed the separation of molecules with only slightly different densities. This enabled parent and daughter strands to be separated and stained using different nitrogen isotopes.
What is theta replication? Which organisms use this sort of replication?
Theta replication is DNA replication in a circular formation used by organisms with circular DNA molecules, like bacteria.
Theta replication begins at a specific origin of replications, and terminates at the TERMINUS OF REPLICATION.
What is the terminus of replication?
the portion where circular dna replication ends.
In circular DNA molecules, replication is __directional from the replication forks
bidirection. it occurs both ways.
In eukaryotes, there are several replication ____ in every chromosome, and the bidirectional replication creates a _____ which fuse together
there are several replication origins in every chromosome, and the bidirectional replication creates a REPLICATION BUBBLE, which fuse together where the forks meet.
What're the two main differences of replication between prokaryotic and eukaryotic DNA?
1) replication and synthesis rate- in eukaryotes, the synthesis is slower, but there are more origins located
2) number of DNA polymerases: Bacteria have 5 different polymerases numbered 1-5, and eukaryotes have at least 15 polymerases, the main ones being sigma, alpha and E
Which 3 polymerases are used for main chromosome replication in eukaryotic cells
sigma, alpha and E
What is the purpose of DnaA protein? is this used by prokaryotic or eukaryotic cells?
it recognizes the PROKARYOTIC origin and begins strand separation
What produces Helicase? What does it do and how does it power this process?
helicase is a protein produced by ecoli gene DNaB, and uses ATP to power the strand separation process once DNaA recognizes the origin.
T/F: Single stranded DNA is unstable and tends to reanneal after separation
What keeps the single stranded DNA from separating?
SSB- single stranded DNA binding protein coats the SS DNA to ensure availability of a template and to protect ssDNA from degradation.
T/F Unwinding the DNA causes tension
What protein relieves the tension from DNA unwinding? How do they do this?
in prokaryotes, protein TOPOISOMERASE catalyzes teh cutting and rejoining of DNA molecules.
What does topoisomerase two do?
topoisomerase II cuts both strands of DNA
Where is gyrase found? what does it do?
gyrase topoisomerase cuts the DNA strands to release tension, swivels the broken strands, relieving the stress and reseal any nicks, allowing helix unwinding to continue.
What stage does origin recognition, unwinding, template stabilization and tension relief of prokaryotic DNA replication fall under?
What protein is needed for DNA Polymerase to initiate DNA synthesis? In prokaryotes, what is it made of? How about in Eukaryotes?
A primer is a short double stranded segment with a 3' hydroxyl, which is needed for initiation. In prokaryotes, it is called a PRIMASE: an RNA primer. in eukaryotes, it is called a PRIMOSOME: a primer made of RNA and DNA.
What is pol III Holoenzyme?
a multiprotein complex used in chain elongation and proofreading in eukaryotes.
What is the beta clamp?
holds the pol III holoenzyme onto the template stand.
What is a replisome?
the entire molecular machine. multiprotein made of composed of a number of proteins including helicase, RFC, PCNA, gyrase/topoisomerase, SSB/RPA, primase, DNA polymerase III, RNAse H, and ligase. The replisome first unwinds double stranded DNA into two single strands. For each of the resulting single strands, a new complementary sequence of DNA is synthesized
What is a 3'-5' exonuclease?
breaks the phosphodiester bond in the sugar-phosphate backbone of a nucleic acid chain and removes the terminal nucleotide FROM THE 3' END if there is an error. aids in proofreading by correcting incorporation errors that occurred during polymerization
a template strand is read in a x' to y' manner, and DNA is synthesized in a y' to x' direction
a template strand is read in a 3' to 5' manner, and DNA is synthesized in a 5' to 3' direction.
Which strand is the leading strand?
the leading strand is the strand that is running in a 3' to 5' manner and can thus be synthesized CONTINUOUSLY in a 5' to 3' manner.
A lagging strand is synthesized in ____ fragments
What is the job of Pol 1 Polymerase? What're the three main enzymatic activities of poly 1 polymerase
it is in prokaryotic e.coli, and it removes the RNA primerase primer and inserts the appropriate deoxyribonucleotides.
1) pol 1 acts as a polymerase: inserts nucleotides in 5'-3' direction
2) pol 1 acts as an exonuclease: proof reads in a 3'-5' manner
3) pol 1 acts as an exonuclease in terms of removing RNA primerase (as mentioned above)