Test 4. Chapter 18 Flashcards
Define DNA polymerase
- enzyme that synthesizes DNA, catalyzes phosphodiester linkage
- proofreading activity
what is a template?
it is a sequence of nucleic acids that determines the sequence of a complementary necleic acid
what is a primer?
it is the initial segment of a polymer that is to be extended on which elongation depends
what are the key characteristics of DNA synthesis?
Four deoxynucleoside triphosphates (dNTPs) and Mg2+ are required.
A template strand is used to direct DNA synthesis.
A primer from which the new strand grows must be present.
Many DNA polymerases have nuclease activity that allows for the removal of mismatched bases.
a template strand is used to ???
direct DNA synthesis
A primer from which _________?
a primer from which the new strand grows must be present
which polymerase is used for replication?
polymerase 3
DNA polymerases catalyze the formation of a phosphodiester bridge. Elongation of the DNA strand proceeds in the __________.
5-to-3 direction
DNA polymerase catalyzes _______________ linkage formation
phosphodiester linkage
DNA replication starts at the ____________-
replication origin
DNA must be locally unwound to expose single-stranded templates for replication. This unwinding puts a strain on the molecule by causing the overwinding of nearby regions.
Need – something to hold strands apart (___________) and something to relieve stress of overwinding (_____________)
helicase
topoisomerase
the separation of DNA strands require __________ and ________-
specific helicases and ATP hydrolysis
Topoisomerase prepare the double helix for _________-
unwinding
What does topoisomerase I do?
what does topoisomerase II do?
Topoisomerase I – relaxes supercoils
Topoisomerase II (aka DNA gyrase in E. coli) - introduces supercoiling
____________ blocks the binding of ATP to gyrase.
Nalidixic acid and ciprofloxacin are inhibitors of DNA gyrase that are used to treat bacterial infections, interfere with breakage and rejoining of DNA strands.
____________ prevents anthrax poisoning.
Novobiocin
Ciprofloxacin
Replication begins in E. coli at the __________
DnaA protein binds and then recruits DnaB, a helicase.
Single-stranded-binding protein (SSB) bind to the AT-rich sites in the locus to prevent reannealing of the helix.
The resulting complex of DNA and proteins is called the prepriming complex.
oriC locus.
RNA polymerase that synthesizes short RNA (≈10 nucleotides) complementary to a DNA strand that then serves as a _______for DNA synthesis.
primer
Assembly of DnaA and formation of the ________
prepriming complex
DNA synthesis on one of the template DNA strands is ___________: new DNA is synthesized in small pieces which then are connected together
discontinuous
DNA synthesis always starts with a ___________
RNA primer
DNA a
primase, initiates replication, generating ~ 20 dNTP
DNA δ
more processive enzyme that extends the chains
DNA δ
more processive enzyme that extends the chains
The free ends of linear DNA molecules present two biochemical difficulties.
???
They are susceptible to damage by nucleases.
Due to the nature of DNA synthesis, one strand will shorten upon each round of DNA synthesis.
Telomeres are replicated by __________________, a speicalized polymerase that carries its own RNA template
telomarase
The G-rich leading strand of the telomere can be maintained by the enzyme telomerase.
Telomerase contains an RNA template that it uses to extend the leading strand.
huntington disease
triple repeat expansion of sequence CAG
high energy electromagnetic radiation, such as __________, may cause breaks in the DNA strands
X-rays
What mechanism does DNA repair systems follow?
Recognize the inappropriate base(s).
Remove the inappropriate base(s).
Fill in the resulting gap with DNA polymerase I and DNA ligase.
The first DNA repair mechanism occurs when DNA polymerase proofread the newly synthesized DNA and correct mismatches.
mismatch repair
systems correct errors not corrected by proofreading.
In E. coli, two proteins are required for mismatch repair―one to recognize the error and one to recruit an exonuclease to cleave the DNA.
Direct repair
corrects mistakes without having to remove any fragments of DNA.
DNA photolyase uses light energy to cleave pyrimidine dimers.
Base-excision repair
corrects modified bases with several enzymes.
The enzyme AlkA removes the base. The site of the missing base is called an AP site.
The DNA backbone at the AP site is cleaved by AP endonuclease and a phosphodiesterase excises the deoxyribose phosphate.
The gap is repaired by DNA polymerase I and DNA ligase.
Base-excision repair corrects the most common point mutation in humans, the deamination of methyl cytosine to thymine.
Mismatch pair
MutS recognizes G-T mismatch
MutH cleaves backbone at mismatch
Exonuclease I removes strand containing mismatch
DNA polymerase III synthesizes new strand
Base excision repair
DNA glycosylase recognizes and excises incorrect base
AP endonuclease recognizes lesion and nicks DNA strand
DNA polymerase and DNA ligase fill the gap
Mismatch repaired
The double strand break is recognized and the________________generating single-strand regions that are bound by RAD51.
____________ occurs when a single strand from the damaged DNA replaces a strand in the undamaged DNA. The resulting three-stranded structure is called a displacement loop.
___________ occurs, using the undamaged DNA as a template.
A __________________ occurs to complete the repair, forming a structure called a Holliday junction.
Cleavage and ligation yield two intact helices.
5’ ends are digested
Strand invasion
DNA synthesis
second strand invasion
_____________ is the exchange of genetic information between two DNA molecules.
_________________ is useful for repair of extensive damage to the DNA, such as breaks in both strands of the DNA.
Recombination
