DNA RNA lect Flashcards
refers to the single units within nucleotides
nucleoside monophosphates
it serves as the precursor molecule during nucleic acid synthesis within the cell
triphosphate form
two long polynucleotide chains are coiled around central axis forming a __
right handed double helix
x-ray diffraction data shows that the DNA is a regular helix and the repeat distance is __
34 A*
average structure should be __
10 base pairs
- more base pairs refer as ___
- fewer base pairs refer as ___
more base pairs = overwound
fewer base pairs = underwound
denaturing agents
formamide or urea
site of interaction with many proteins that will bind to the specific nucleotides
binding or recognition sites
DNA molecule that exists in a very high relative humidity environment (92%)
B-DNA
Watson-Crick DNA
how many base pairs in each turn for B-DNA and the length of one turn of helix
10 base pairs
34A
DNA is dehydrated or under high salt conditions
A-DNA
which is short and thicker form of DNA?
A-DNA
how many base pairs in each turn for A-DNA and the repeat double helix
11 base pairs
24.6 A
a left handed, longer and narrower form of DNA in which it is known to occur in nature when there is a sequence of alternating purinepyrimidine
Z-DNA
how many base pairs in each helical turn for Z-DNA and the repeat helix
12 base pairs
45.6 A
Z-DNA is formed under conditions of __
high salt / presence of alcohol
DNA is duplicated __ cell division
before cell division
a stage in the cell cycle in which the replication undergo
S phase
structure that unwind the double helix in opposite directions
replication fork
phase in which the replication machinery moves along the parent dna strands and forms the daughter strands
adding of nucleotides
elongation phase
what phase does the two replication forks moving in opposite directions meet
termination phase
sites at which single stranded DNA is exposed and at which DNA synthesis occurs
replication forks
an enzyme that synthesize the short RNA sequences that are complementary to a single stranded piece of DNA which serves as its templates
primase
why there is a primase?
DNA polymerase cannot synthesize nucleotide without a based template
protein complex that serves as a processivity-promoting factor in DNA replication.
sliding clamp (beta clamp)
these protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand
sliding clamp
major enzyme that is the one that polymerize the nucleic acid chain.
DNA polymerase
enzyme responsible for sealing the nick between the new strands and the synthesized by polymerase III and polymerase I.
ligases
these will proposed the semidiscontinuous replication mechanism
okazaki fragments
okazaki fragments will linked this enzyme to form the second daughter strand
DNA ligase
enzyme that harnesses the chemical energy from the ATP hydrolysis to separate the two DNA strands at the replication fork
helicase
these proteins will bind selectively to single-stranded DNA as soon as it forms
Single-strand binding protein
it allows enzymes to attach to the newly opened single strand and initiate elongation and these proteins are removed as DNA synthesis proceeds
Single-strand binding protein
essential bacterial enzyme that catalyzes the ATP-dependent negative super-coiling of double-stranded closed- circular DNA
gyrase (topoisomerase TYPE 2)
responsible for copying a short stretch of the DNA template strand to produce the RNA primer sequence
primase
bind in a complex with the DNA polymerase
primases and alpha catalytic subunit
subunits for eukaryotic primase
- alpha catalytic subunit
- accessary subunit
synthesizes a stretch of 10–30 nucleotides of RNA.
polymerase-α subunit-primase complex
broad class of enzymes that cleave off nucleotides one at a time from the three prime or five prime ends of DNA and RNA chains; it also functions to protect the sequence of nucleotides, which must be faithfully copied
exonucleases
exonuclease function gives the enzyme the capacity to proofread newly synthesized DNA
First polymerase enzyme to direct during the initial synthesis
DNA polymerases III
this is so called okazaki maturation process
DNA polymerase I
uses its polymerase activity to fill in the gap left by the RNA with new DNA.
DNA polymerase I
mass and number of subunits for the DNA polymerase I of E coli
mass: 103 kDa
subunits: 1
mass and number of subunits for the DNA polymerase II of E coli
mass: 90
subunits: >4
mass and number of subunits for the DNA polymerase III of E coli
mass: 830
subunits: >10
This enzyme will add nucleotides to the end of a DNA strand in the absence of hydrogen base pairing with a template. it can synthesize polynucleotide chains without a template
terminal transferase
the only dna polymerase that has 5’ - 3’ exonuclease activity
DNA Pol I
often used in vitro as a method to introduce labeled nucleotides into DNA molecules. The resulting labeled products are used for DNA detection in hybridization analyses.
cut-and-patch nick translation
responsible for the coupling of DNA replication. this is composed of DNA polymerase, sliding clamp, and clamp loader.
replisome
responsible for holding catalytic cores onto their template strands.
sliding clamp
recruiting DNA polymerase to the appropriate location on the DNA template. They localize specifically at the region where DNA synthesis needs to commence.
clamp loader and sliding clamp
associated with the clamp loader and links this polymerases-clamp loader complex to the helicase.
Tau protein
enzymes that modulate in the degree of DNA supercoiling. They can also convert one isomer of DNA to another
topoisomerases
a topoisomerase enzymes transiently cleave and reseal one strand of duplex DNA in the absence of ATP
TP 1
topoisomerase enzymes will cleave and relegate both DNA strands in the presence of ATP.
TP 2
- TTGGGG
- TTAGGG
- protozoans
- vertebrates
endonucleases that recognize specific base sequences and break or restrict the DNA polymer at the sugar-phosphate backbone
restriction enzymes
most frequently used restriction enzyme in the lab
RE type II
- cleave the DNA directly at the binding site, producing fragments of predictable size.
- Analysis of gene rearrangements
- Mutation detection
- DNA recombination in vitro
- Mapping a DNA fragment
uses of restriction enzymes
the targets for several anticancer drugs. These __ inhibitors bring about cell death by interfering with the breaking and joining activities of the enzymes, in some cases trapping unfinished and broken intermediates
topoisomerase
catalyze the addition of methyl groups to nitrogen bases, usually adenines and cytosines in DNA strands
methylation
slipped structures, cruciform, and triple-helix
secondary structures
the middle point of a temperature range where 50% of your DNA strands are denatured and the amount of denatured DNA is measured at an absorbance of __ nanometer.
melting temperature
260 nm
DNA supercoiling is the __ winding of DNA helix axis that occurs when the double helix is under or over wound.
tertiary
