Week 4 Textbook Flashcards
what are the two special qualities of DNA Polymerase to increase accuracy
- enzyme monitoring the base-pairing between each incoming nucleoside triphosphate and the template strand
- DNA polymerase does make a rare mistake and adds the wrong nucleotide - but can correct this error through proofreading
explain DNA polymerases proof reading function
takes place at the same time as DNA synthesis
- before the enzyme adds the next nucleotide to a growing DNA strand - it checks whether the previous nucleotide was added correctly relative to the template strand
- if it is wrong, they pause to clip it off and then tries again
- the polymerase and the proof reading are two reactions that are carried out by different catalytic domains in the same polymerase molecule - its in a separate area in the molecule
why does proof reading work only in the 5’ to 3’ direction
if DNA synthesized in the 3’ to 5’ it would not be able to proofread
-if the wrong polymerase were to remove an incorrect paired nucleotide from the 5’ end it would create a chemical dead end - which is a strand that can’t continue to be added onto or elongated
- the backstitching mechanism on the lagging strand is necessary consequence of maintaining proof reading
what is primase
it is made from a short length RNA which acts as primer for DNA synthesis
- primase synthesized into the 5’ to the 3’ which is the 3’ to 5’ on the template strand
- this primase can act as a RNA polymerase which is synthesized on the DNA template strand since they are chemically very similar (except for the ribose sugar instead of the deoxyribose and for the U base pair)
- U and A can bind
T/F for the leading strand, an RNA primer is needed only to start replication at a replication origin
true
- at this origin point, the DNA polymerase takes over and extends this primer with DNA synthesized in the 5’ to 3’ direction
but in the lagging strand - they are needed continuously to prime the Okazaki fragments and keep the polymerization going
the RNA primer must be laid down on the newly exposed single-stranded DNA stretch
- the primer is added to the 5’ end of the fragment
T/F previous RNA primer removed by nuclease and replaced with DNA by repair polyermase
true
the primer is removed (only temporarily)
and the gap is sealed by DNA ligase
what are the enzymes that work together to remove the RNA primer and replace it with DNA
- a nuclease degrades the RNA primer
- repair polymerase replaces the primers with DNA (using the end of the okaxaki fragment as its primer
- DNA ligase joins the 5’ phosphate end to the DNA fragments 3’ hydroxyl end
which part is known as DNA polymerase 1
repair polymerase
since it was discovered first
which part is known as DNA polymerase 3
the polymerase that carries out the bulk of DNA replication at the forks
T/F there is no primase proofreading
true
because it is already made out of RNA instead of DNA they stand out and are automatically removed and replaced with DAN
- the repair polymerase = 1 already proof reads it when it synthesizes
what does DNA helicase do
it is the first step to the replication machine where it unzips the DNA helix so that the nucleotides are exposed
- it uses the energy from ATP hydrolysis
what does single strand DNA binding proteins do
they latch onto the single-stranded DNA exposed by the helicase, preventing the strands from re-forming base pairs and keeping them in an elongated form so that they can serve as efficient templates for the DNA polymerase to use
what is the need of DNA topoisomerase
when DNA helicase is unzipping DNA, the secured helix above waiting to be unzipped can get supercoiled with itself and creates torsional stress to build up
DNA topoisomerase create a single-stranded break where the rotation occurred
once the super coiling has relieved itself, it reseals the same area so that the DNA helicase can occur properly
what is a sliding clamp
it keeps DNA polymerase firmly attached to the template while it is synthesizing new strands of DNA
- without something clamping the polymerase to the strand it falls off after a while
- it forms a ring around the newly formed DNA double helix and by gripping the polymerase - it allows the enzyme to move along the template strand
what does the clamp loader do
hydrolyzes ATP each time it locks a sliding clamp around a newly formed DNA double helix
- it is added only once per replication cycle on the leading strand - on the lagging strand - the clamp is removed so that new single stranded DNA can pass thru the helicase, an RNA primer can be placed, and single stranded binding proteins can be added, then the clamp is re added so the polymerase can work its backstitching mechanisms to build the other strand beginning at the primer and remove the proteins until it reaches the adjacent Okazaki fragment (cycle repeats)
what happens when the replication fork approaches the end of the chromosome?
on the leading strand, the replication can be all the way to the tip but the lagging strand cannot
when the final RNA primer is added onto the lagging strand - it is removed and there is no enzyme to replace it with DNA
- without a process to fix this the lagging strand would become shorter with each round of DNA replication after each cell division
- the chromosomes would shrink and lose valuable genetic information
why don’t bacteria have the issue with the end replication problem
their chromosomes are circular so they have no ends
what are telomers
they add long, repetitive nucleotide sequences to the end of every chromosome to give the lagging strand extra DNA
what is telomerase
an enzyme that carries its own RNA template which is used to add multiple copies of the same repetitive DNA sequence to the lagging strand template
- telomeres also always replenished when division occurs
T/F telomers attract telomerase and other telomere binding proteins
true
they protect the chromosome ends
and help maintain telomere length
how do telomers tell us how often a cell divides
the area with cells that are always dividing like muscle cells, they have fully active telomerase that replenishes the telomer
- many other cell types reduce their telomerase activity after many rounds of cell division - when the telomer disappears the cell no longer divides
- this can act as a controller on the divison of cells which can help cancer
what is depurination
spont reaction
- remove a purine base from a nucleotide by being lost in water molecules that have bombarded the DNA in the cells of your body
- leads to an area with a missing piece
what is deamination
loss from the reaction of water
spont reaction
loss of an amnio group from a cytosine in DNA to produce a base of Uracil
how does UV in sunlight damage DNA
it promotes covalent linkage between two adjacent pyrimidine bases
forming for example a thymine dimer (two thymine bases being bonded together)
- it is the failure to repair the thymine dimers that = disease
T/F chemical modification of nucleotides can cause permanent mutations
if they are left unfixed, they can
- deamination - without fixing can lead to substitution of one base for another when the DNA is replicated
- depurination - without fixing can lead to the loss of a nucleotide pair - when the replication process occurs the machine can skip over the incomplete nucleotide
T/F when one strand is accidently damaged the information is not completely lost
true
because there is a template strand that can easily code for the other new strand
explain the steps that occur when an area of a strand is damaged
the segment that is damaged is removed and left as a gap
- the DNA polymerase 1 binds to the 3’ hydroxyl end of the cut DNA strand - fills in the missing nucleoside using the bottom strand as a template (or vise versa)
- DNA ligase seals the gap and the damage is repaired
what is the system called mismatch repair?
the cell backup system to its proofreading abilities
- correcting the errors
whenever the replication machinery makes a copying mistake, it leaves behind a mispaired nucleotide = mismatch
if left undetected - the complex of mismatch repair proteins will detect the DNA mismatch - remove a portion of the newly synthesized missing DNA
how does the mismatch repair system work
- it must be able to recognize which of the two DAN strands contains the error
- they make sure they are removing the correct one by monitoring only the newly made DNA
how is mismatch repair important in preventing cancer in humans
humans have 2 copies of these mismatch repair proteins
- the individual is not affected until the undamaged copy f the same gene is randomly mutated in a somatic cell
- the mutant cell and all its progeny are deficient in the mismatch repair
- they accumulate mutations = cancerous
what are the 4 different types of DNA repair systems
- direct repair
- converts them back to their original kind - excision repair
- minor damage that is cut out of the nucleotide by using DNA glycosylase and then flips the base on the outside - cuts it and is replaced and ligased
- fix damaged nucleotides damaged by mutagens - mismatch repair
- errors from the replication process
- can be distinguished by methylation
- the helicase unzips the area, DNA polymerase 1 adds back the nucleotide and ligased together - nonhomologous end joining
- used to mend double stranded breaks in DNA (caused by radiation, chemical assaults, etc which can lead to a loss of information)
- quickly sticking the 2 halves back together by ligase “quick and dirty” - lost some nucleotides - homologous recombination
what is a mutation
the replication and repair process can fail and allow for a permeant change in the DNA sequence which can have good, neutral or bad impacts
- a mutation that codes for the wrong protein or eliminates the ability of that protein to function (sickle-cell anemia)
- mutations to hemoglobin gene can produce a protein that is less soluble than normal hemoglobin which = sickle cell shapes RBCs
- it can cause death but also make them resistant to malaria
T/F mutations in the reproductive germline can cause the mutation to be passed on to all the cells in the body
true
even the gametes responsible for the production of the next generation
t/f mutations can occur during the life of an individual
true
nucleotide changes that occur in somatic cells can give rise to variant cells which grow and divide in an uncontrolled fashion at the expense of the other cells in the organism
- cancer = accumulation of gradual and random mutations in the somatic cells
cancer incidence increases with age
how does natural selection work on the mutations that are harmful
those who carry these harmful mutations usually die and don’t get to pass on these mutations to their offspring = eliminated from the population
what happens to the mutations that are neutral
no effect on fitness of the organism = preserved for a very long time
= variation
