Lecture 6: DNA Metabolism Flashcards
ispA
Gene or Protein
Gene
IspA
Gene or Protein
Protein
Meselson-Stahl demonstrated what in regards to the structure of DNA
Semi-conservative; there are two strands of DNA
______(Enzyme) ___ are responsible for replication
DNA Polymerase
DNA Template runs in what direction?
3” -> 5’
DNA Primer run-in what direction?
5’ -> 3’
DNA Polymerase runs in what direction?
5’ -> 3’
How does DNA Polymerase bind to the stand? What mechanism occurs?
DNA Polymerase attacks alpha-phosphorous group
Phosphate group comes off
Forms a phosphodiester bond
DNA Polymerase utilizes single stranded DNA templates and adds nucleotides to a growing chain in the _____ direction.
5’ -> 3’ direction
What is the ORI (Origin of Replication?
Unique point where DNA replication begins
What type of N-Bases are found at the ORI?
A-T rich
E. Coli replicates using what mechanism?
Replication Bubbles
Replication forks travel in what direction?
Bidirectional
The branch point in a replication bubble is called _______.
Replication Fork
New DNA is added to which end of the strand?
3’ end
Leading Strand reads?
5’ -> 3’
Lagging Strand reads?
3’ -> 5’
What is DNA Ligase?
Enzyme that seals/joins the discontinuous Okazaki fragments together into a continuous piece of DNA
Okazaki Fragments are found on which strand?
Lagging
What is Primase?
Synthesize RNA Primers
What is semi-conservative replication?
Each strand includes one parent strand and one newly synthesized daughter strand
What is exonuclease?
Remove DNA only from the ends of DNA strands
What is endonuclease?
Degrade DNA from the interior of a DNA strand by hydrolyzing the phosphodiester bond)
What are restriction enzymes?
The specified sequences where endonuclease cut internally
What is DNA Polymerase?
Enzyme that synthesize DNA
True or False
DNA Polymerase will polymerase 5’ -> 3’
True
DNA Polymerase is an favorable or unfavorable?
Favorable
exergonic
(-) Delta G
Does DNA Polymerase require a primer?
Yes
E. coli DNA polymerase III:
A) can initiate replication without a primer.
B) is efficient at nick translation.
C) is the principal DNA polymerase in chromosomal DNA replication.
D) represents over 90% of the DNA polymerase activity in E. coli cells.
E) requires a free 5’-hydroxyl group as a primer
C
ORI is A-T rich or G-C rich?
A-T
. The Meselson-Stahl experiment established that:
A) DNA polymerase has a crucial role in DNA synthesis.
B) DNA synthesis in E. coli proceeds by a conservative mechanism.
C) DNA synthesis in E. coli proceeds by a semiconservative mechanism.
D) DNA synthesis requires dATP, dCTP, dGTP, and dTTP.
E) newly synthesized DNA in E. coli has a different base composition than the preexisting DNA.
C
When a DNA molecule is described as replicating bidirectionally, that means that it has two:
A) chains. B) independently replicating segment. C) origins. D) replication forks. E) termination points.
d
An Okazaki fragment is a:
A) fragment of DNA resulting from endonuclease action.
B) fragment of RNA that is a subunit of the 30S ribosome.
C) piece of DNA that is synthesized in the 3’—>5’ direction.
D) segment of DNA that is an intermediate in the synthesis of the lagging strand.
E) segment of mRNA synthesized by RNA polymerase.
d
The proofreading function of DNA polymerase involves all of the following except:
A) a 3'--->5' exonuclease. B) base pairing. C) detection of mismatched base pairs. D) phosphodiester bond hydrolysis. E) reversal of the polymerization reaction.
E
The 5’—>3’ exonuclease activity of E. coli DNA polymerase I is involved in:
A) formation of a nick at the DNA replication origin.
B) formation of Okazaki fragments.
C) proofreading of the replication process.
D) removal of RNA primers by nick translation.
E) sealing of nicks by ligase action.
D
Prokaryotic DNA polymerase III:
A) contains a 5’—>3’ proofreading activity to improve the fidelity of replication.
B) does not require a primer molecule to initiate replication.
C) has a beta subunit that acts as a circular clamp to improve the processivity of DNA synthesis.
D) synthesizes DNA in the 3’—>5’ direction.
E) synthesizes only the leading strand; DNA polymerase I synthesizes the lagging strand.
C
Which of the following is not required for elongation during DNA replication in E. coli?
A) DnaB (helicase) B) DnaG (primase) C) DnaC D) Beta-sliding clamp E) Clamp loader
C
The function of the eukaryotic DNA replication factor PCNA (proliferating cell nuclear antigen) is similar to that of the -subunit of bacterial DNA polymerase III in that it:
A) facilitates replication of telomeres.
B) forms a circular sliding clamp to increase the processivity of replication.
C) has a 3’—>5’ proofreading activity.
D) increases the speed but not the processivity of the replication complex.
E) participates in DNA repair.
B
. In a mammalian cell, DNA repair systems:
A) are extraordinarily efficient energetically.
B) are generally absent, except in egg and sperm cells.
C) can repair deletions, but not mismatches.
D) can repair most types of lesions except those caused by UV light.
E) normally repair more than 99% of the DNA lesions that occur.
E
Which of these enzymes is not directly involved in methyl-directed mismatch repair in E. coli?
A) DNA glycosylase B) DNA helicase II C) DNA ligase D) DNA polymerase III E) Exonuclease I
A
. Which mechanism is used to repair a thymidine dimer in DNA?
A) Mismatch repair B) Base-excision repair C) Nucleotide-excision repair D) Direct repair E) More than one is used for this type of lesion
D
Which mechanism is used to repair a chemically modified base in DNA?
A) Mismatch repair B) Base-excision repair C) Nucleotide-excision repair D) Direct repair E) More than one is used for this type of lesion
E
In homologous recombination in E. coli, the protein that assembles into long, helical filaments that coat a region of DNA is:
A) DNA methylase. B) DNA polymerase. C) histone. D) RecA protein. E) RecBCD enzyme.
D
Which of the following is not a feature of homologous recombination during meiosis?
A) A double strand break
B) Cleavage of two crossover events
C) Alignment of homologous chromosomes
D) Formation of a single Holliday intermediate
E) Exposed 3’ ends invade the intact duplex DNA of the homolog
D
True or False;
Most polymerases have 3’ -> 5’ exonuclease activity, which is used to remove incorrect bases; proofreading capability
True
In E. Coli, DNA Polymerase III is ___
Replication Enzyme.
In E. Coli, DNA Polymerase I is ____.
clean up functions during replication, recombination and repair.
In E. Coli DNA Polymerase II, IV, and V ___.
DNA Repair
In E. Coli, which DNA Polymerase is the fastest?
Polymerase III
In E. Coli, Which DNA Polymerase participates in nick translation?
DNA Polymerase I