DNA Replication and Repair Flashcards
genome
all the DNA in an organism, including genes and non coding parts
plasmids
accessory replicating DNA molecules
chromosome
a dna molecule with part or all of the genetic material of an organism
T/F a chromosome contains all the essential genetic information for life
true
T/F chromosomes are usually linear in humans and circular in bacteria
t
T/f plasmids are smaller than chromosomes
true
genes
parts of DNA that are transcribed
T/F virus genomes can be RNA or DNA
t
____ are the simplest cellular life forms, can be free-living or obligate endosymbionts of other host cells
prokaryotes (arcaea and bacteria)
prokaryotes genomes typically range from __ to ___ genes
400 to 9 000
T/F most genes in prokaryotes are found in a single circular chromosome
true
t/f some bacteria have multiple chromosomes and linear chromosomes
true
eukaryotic dna is wrapped around proteins called __
histones
dna wrapped around a histone is collectively called a __
nucleosome
the formation of nucleosomes contributes to the ___ of dna
packing
nucleosomes arrange into helical stacks called __
chromatin
folding of chromatin creates __
chromosomes
t/f chromosomes are the highest condensed structures
t
structure of chromatin during interphase and reason for this structure
loose; allowing DNA polymerase to get at the genes
during which cell stage is dna copied in preparation for mitosis?
interphase
in which stage of the cell cycle do chromosomes condense from chromatin? why?
metaphase ; to ease the separation of daughter cells
what % of the human genome is coding?
1.5%
protein coding DNA in humans is __%
2
how many exons/introns in bacterial genes
one exon, no introns
how many exons/introns in eukaryotic genes
multiple axons and introns
introns nad exons are ___ with a gene
nucleotide sequences
introns are removed by ___
RNA splicing
exons are covalently bonding to each other to make __
mRNA
DNA replication is semi-conservative, meaning :
each daughter cell gets a copy of DNA that is half from the parent and half newly made
the new DNA is assembled directly on a ___
pre-existing DNA template
role of helicase:
separates the dna strands making a fork with 2 template strands
role of single strand binding proteins (ssb)
stabilize the strands and prevent annealing
role of primase
creates RNA primers, required to start replication
role of DNA polymerase iii
binds at primer, builds the complementary strand from there
role of DNA polymerase 1
removes primers as dns polymerase 3 approaches it
dna polymerase 1 is especially important in the __ strand
lagging
role of dna ligase
joins Okazaki fragments by joining phosphodiester bonds between adjacent nucleotides
what enzymes unwinds dsdna in front of DNA polymerase?
helicase
helicase is made of how many subunits?
3 different, 6 total
t/f helicase is a hexamer
t
SSbs are removed when ___ approaches
polymerase 3
what is an RNA primer?
short RNA segment that allows the polymerase to start replication
dna polymerase 3 catalyzes the step-by-step addition of __ to a dna strand
deoxyribonucleotide
DNA polymerase makes dna in the ___ direction
5’ –> 3’
DNA polymerase requires what 4 things?
- a template strand of dna
- a primer
- precursors
- mg 2+ cofactors
primers initiate __
transcription
what are precursors?
the building blocks of the dna product: the deoxyribonucleotide triphosphate
DNA + dNTP =
dna + pyrophospate ion
the strand elongation reaction catalyzed by polymerases is a nucleophilic attack by the ___ end of the growing strand to the ___ of dNTP
3’OH ; innermost phosphorus atom
the 2 Mg increase the ___and help the position of __ in the active site
nucleophilicity of attacking OH; phosphates
after attack by OH, a ___ bridge is formed and ___ is released
phosphodiester; pyrophosphate
what happens to the released pyrophosphate that drives the polymerization forward?
hydrolyzed into 2 orthophosphates
the basic structure of DNA polymerases resembles what anatomical structure/
an open right hand
the “palm” of a dna polymerases contains ___
DNA, catalytically essential amino acids
the “fingers” of dna polymerases are essential for __
nucleotide recognition and binding
the “thumb” of dna polymerases are important to __
binding of the DNA substrate (dNTPs)
the upper strand is the ___ strand; replication is ___
leading ; continuous
the lower strand is the ___ strand ; replication is ___
lagging; discontinuous
what part of DNA polymerase 1 removes the RNA primer?
the exonuclease
dna polymerase 3 disengages when ___
the 2 okazaki fragments meet
role of DNA ligase
joins the Okazaki fragments
ligase catalyzes the formation of a phosphodiester bond between ___ at the end of one dna chain and the ___ at the end of the other
3’OH group; 5’ phosphoryl
DNA damage can be thought of in what 2 ways?
- errors during replication
2. chemical changes to the nucleotides after replication
what is non-watson-crick base pairing?
when dna incorporates the wrong nucleotide
what is the effect of non-watson crick base pairing on the dna double helix?
local distortion
what does it mean if a non-watson crick base pairing is mutagenic?
results in permanent changes in DNA sequence
when a double helix containing a non-watson-crick base pairing is replicated, the 2 daughter cells will have __ sequences because __
different; the mismatched base is likely to pair with its Watson crick partner
the ___ subunit of DNA polymerase 3 core has ___ activity that can remove an incorrect nucleotide
epsilon; exonuclease
exonuclease
enzyme that removes successive nucleotides from the end of a polynucleotide molecule
alfatoxin
hydrocarbon molecule and a toxin produced by molds that grow on food, like peanuts
in the cell, aflatoxin is converted to an activated form that can modify ___ in DNA
guanine residues
aflatoxin frequently leads to the conversion of a G-C into a ___ mutation
A-T
mis-matches in dna can be repaired by a process called __
mis-match repair
2 enzymes __ and ___ can recruit an enzyme __ that cuts the single strand near the mis-match. A __ then cuts away the single strand with the mis-match
MutS and MutL; MutH; exonuclease
electromagnetic radiation, such as UV light induces ___ between adjacent pyrimidines along one strand of DNA
cross-links
pyrimidine dimers are the primary cause of ___ in humans
melanomas
the ____ repair system can recognize and excise thymine dimers
UvrABC excinuclease
high fidelity in dna replication is maintained by what 3 things?
- accuracy of DNA polymerase
- proof-reading
- mismatch repair