Week 4 Readings Flashcards
do errors in base pairing occur by DNA polymerase?
yes; though A-T and C-G are the most stable pairs, less stable base pairs like G-T and C-A can also be formed
what two qualities does DNA polymerase possess that greatly increase the accuracy of DNA replication?
- only when the base-pairing between each incoming nucleoside triphosphate and the template strand is correct does the DNA polymerase undergo a small structural rearrangement that allows it to catalyse the nucleotide-addition reaction
- when it mistakenly adds the wrong nucleotide, it can correct this error via proofreading
describe proofreading
- before the enzyme adds the next nucleotide to a growing DNA strand, it checks whether the previously added nucleotide is correctly base-paired to the template strand
- if so, the polymerase adds the next nucleotide; if not the polymerase pauses to clip off the misfired nucleotide and then tries again
why can the proofreading mechanism only be performed by DNA polymerase in the 5’ to 3’ direction?
if a DNA polymerase were able to synthesise in the 3’ to 5’ direction, if this ‘backward’ polymerase were to remove an incorrectly paired nucleotide from the 5’ end, it would create a chemical dead end - a strand that could no longer be elongated. this is because removal of an incorrect nucleotide would stop replication, as there would be no high-energy phosphodiester bond to drive the addition of the next nucleoside triphosphate
describe the role of primase
makes a short length of RNA, about 10 nucleotides long, base-paired to the template strand, which provides a base-paired 3’ end as a starting point for DNA polymerase
describe how RNA primers are used differently for the leading and lagging strands
Leading strand: an RNA primer is needed only to start replication at a replication origin
Lagging strand: new primers are continuously needed. DNA polymerase adds a deoxyribonucleotide to the 3’ end of each new primer to produce an Okazaki fragment, and it will continue to elongate this fragment until it runs into the previously synthesised RNA primers
describe the enzymes that join the newly synthesised DNA together
- a nuclease: degrades the RNA primer
- DNA polymerase I: a repair polymerase that replaces the RNA primers with DNA
- DNA ligase: joins the 5’ phosphate end of one DNA fragment tot he adjacent 3’ hydroxyl end of the next
does primase proofread its work?
no, but the repair polymerase that makes the DNA replacing the primers does
why does localised unwinding of the DNA double helix present a problem?
as the helicase moves forward, prying open the double helix, the DNA ahead of the fork gets wound more tightly, creating tension
DNA polymerase
catalyses the addition of nucleotides to the 3’ end of a growing strand of DNA using a parent DNA strand as a template; proofreads nucleotides added to newly synthesised DNA and removes those that are paired incorrectly
DNA helicase
uses the energy of ATP hydrolysis to pry apart the DNA double helix ahead of the replication fork
single-strand DNA binding protein
binds to single-stranded DNA exposed by DNA helicase, preventing base pairs from re-forming before the lagging strand can be replicated
DNA topoisomerase
produces transient breaks in one strand of the DNA double helix to relieve the tension built up by the unwinding of DNA ahead of the DNA helicase; reseals breaks after DNA has relaxed
sliding clamp
keeps DNA polymerase attached to the template, allowing the enzyme to move along without falling off as it synthesises new DNA
clamp loader
uses the energy of ATP hydrolysis to lock the sliding clamp onto DNA
primase
synthesises RNA primers along the lagging-strand template
DNA ligase
uses the energy of ATP hydrolysis to join Okazaki fragments made on the lagging-strand template
what is the issue with replicating the very ends of linear chromosomes?
- although the leading strand can be replicated all the way to the chromosome tip, the lagging strand cannot
- when the final RNA primer on the lagging strand is removed, there is no enzyme that can replace it with DNA
- without a strategy to deal with this, the lagging strand would become shorter with each round of DNA replication, and the chromosomes would shrink
why are bacteria not subject to the end-replication problem?
their chromosomes are circular DNA molecules
describe telomeres
structures incorporating long, repetitive nucleotide sequences at the ends of every chromosome. they attract telomerase to the chromosome ends
describe the function of telomerase
carries its own RNA template, which it uses to add multiple copies of the same repetitive DNA sequence to the lagging-strand template
what is a secondary function of telomeres?
mark the true ends of a chromosome; this allows the cell to distinguish between the natural ends of the chromosomes and the double-strand DNA breaks that sometimes occur accidentally in the middle of chromosomes
how is telomere control involved in the prevention of the development of cancer?
- cells that divide at a rapid rate throughout the life of the organism (ie bone marrow) keep telomerase fully active
- others gradually reduce telomerase activity, causing telomeres in descendant cells to shrink until they disappear. at this point, the cells will cease dividing
depurination
purine bases are lost as water molecules bombard the DNA in the cells of the body. This does not break the DNA phosphodiester backbone but removes a purine base from a nucleotide and gives rise to lesions
deamination
a common reaction with water that causes the spontaneous loss of an amino group from a cytosine in DNA to produce the base uracil
how is UV radiation damaging to DNA?
promotes covalent linkage between two adjacent pyrimidine bases (ie forming a thymine dimer)
what can unprepared DNA damage lead to?
- substitution for one nucleotide pair for another during replication
- deletion of one or more nucleotide pairs int he daughter DNA strand after replication
- some types of damage may stall the DNA replication machinery at the site of the damage
describe the basic pathway for repairing damage to DNA
- the damaged DNA is recognised and removed by a variety of nucleases that cleave the DNA backbone around the damage, leaving a small gap on one strand of the DNA double helix.
- a repair DNA polymerase binds to the 3’-hydroxyl end of the cut DNA strand. the enzyme then fills in the gap by making a complementary copy of the information present in the undamaged stand
- when the repair DNA polymerase has filled in the gap, a break remains in the sugar-phosphate backbone of the repaired strand. this break is sealed by DNA ligase
what is the use of a mismatch system?
a backup system to the proofreading abilities of the replication machinery
describe how mismatch systems work
- whenever the replication machinery makes a copying mistake, it leaves behind a misfired nucleotide (a mismatch)
- a complex of mismatch repair proteins will detect the DNA mismatch, remove a portion of the newly synthesised DNA strand containing the error, and then resynthesises the missing DNA
how do mismatch systems recognise which of the two DNA strands contains the error?
it reorganises and removes only the newly made DNA
what is the role of mismatch systems in preventing cancer?
- an inherited predisposition to certain cancers is caused by mutations in mismatch repair protein genes
- individuals who inherit a single damaged mismatched repair gene are unaffected until the undamaged copy is randomly mutated in a somatic cell
- the mutant cell and all of its progeny are then deficient in mismatch repair; they thus accumulate mutations more rapidly
define a double-strand break
when both strands of a DNA segment are damaged at the same time
why are double strand breaks particularly dangerous?
they can lead to the fragmentation of chromosomes and the subsequent loss of genes
non homologous end joining
- hurriedly sticking the two broken ends of damaged DNA back together
- however, nucleotides are often lost at the site of repair
- alternative to homologous recombination
Give an example of the impacts of a mutation
- if the change occurs in a particular position in the DNA sequence, it could alter the amino acid sequence of a protein in a way that reduces or eliminates that protein’s ability to function
- sickle cell anaemia is caused by mutation of a single nucleotide in the human haemoglobin gene
distinguish between germ-line and somatic mutations
- a mutation in a germ-line cell will be passed on to all the cells in the body of the multicellular organism that develop from it, including the gametes responsible for the production of the next generation
- somatic cell mutations arise during the life of the individual; unchecked proliferation may lead to cancer
