Ch. 6 Learning Objectives Flashcards
Explain how a DNA double helix provides a template for its own replication
because DNA has complimentary base pairs
describe the resulting daughter helices in terms of their sequence and the distribution of parental and
newly synthesized DNA strands.
the daughter DNA has one of the original (old) and one strand that is completely new. (semiconservative)
Recall where along a chromosome DNA synthesis begins (ori)
the initiator protein binds to specific DNA sequences called replication origins
function of initiator protein
The initiator protein pry the 2 DNA strand apart breaking
the hydrogen bonds between the bases.
explain what characterizes these nucleotide sequences (ori) in simple cells such as bacteria and yeast.
- replication origins span approximately 100 nucleotide
pair - composed of DNA (A-T basepairs) that attract initiator proteins
why do initiator proteins like to bind to DNA rich in A-T basepairs
they are easier to break because they only have 2 H bonds they have to break
Compare the direction in which replication forks move with the direction in which the new
DNA strands are synthesized.
- The 2 forks moves away from the origin in opposite directions
- DNA replication in both bacterial
and eukaryotic is bidirectional.
Do prokaryotes or eukaryotes replicate faster
Prokaryotes because eukaryotes have a more complex chromatin structure
Compare the bonds that link together nucleotides in a DNA strand with the bonds that hold
together the two strands of DNA in a double helix.
- Covalent bonds occur within each linear strand and strongly bond the bases, sugars, and phosphate groups
- Hydrogen bonds occur between nucleotides
Explain how nucleoside triphosphates provide the energy for DNA synthesis
is provided by the incoming deoxyribonucleoside triphosphate itself
Explain why an asymmetrical replication fork poses a challenge for DNA polymerization
- one strand is 5’ –3’ and the other 3’-5’ at each replication fork. This causes an issue with DNA replication as it makes it impossible to synthesized straight forward.
how DNA polymerase solves the asymmetrical replication fork problem to keep the replication fork moving forward
- all DNA polymerases add new subunits only to the 3’ end of a DNA strand. A new DNA chain can be synthesized only in a 5’-3’ direction.\
- for the (3’-5’) strand, DNA uses the “backstitching” maneuver.
the primers required for DNA replication leading strand
- rna primer is needed only to start replication at the replication origin then DNA polymerase takes over.
the primers required for DNA replication lagging strand
- new rna primers are continuously needed
to keep polymerization going. - DNA polymerase then adds a deoxyribonucleotide to the Okazaki fragments until it runs into the previously synthesized RNAprimer.
what 3 additional enzymes are need to join these Okazaki fragments together:
- nuclease
- DNA repair polymerase
- DNA ligase
nuclease function
degrade the RNA primer.
DNA repair polymerase function
replace the RNA primers with
DNA
DNA ligase function
join the 5’-phosphate to the 3’-hydrolxly
Name 7 proteins that form part of the replication machine
- DNA polymerase
- DNA helicase
- Single-stranded DNA- binding protein (SSB)
- DNA topoisomerase
- Sliding clamp
- Clamp loader
- DNA ligase
DNA polymerase role in DNA replication
catalyzes the addition of nucleotides to the 3’ end of a growing strand of DNA strand as a template.
DNA helicase role in DNA replication
uses the energy of ATP hydrolysis to unwind the DNA double helix ahead of the replication fork.
SSB role in dna replication
Binds to single-stranded DNA, preventing base pairs from re-forming before the lagging strand can be replicated.
DNA topoisomerase role in dna replication
produces transient nicks in the DNA backbone to relieve the tension built up by the unwinding of DNA ahead of the DNA helicase.
sliding clamp role in dna replication
Keeps DNA polymerase attached to the template
clamp loader role in dna replication
uses the energy of ATP hydrolysis to lock the sliding clamp onto DNA
DNA ligase role in dna replication
uses the energy of ATP hydrolysis to join Okazaki fragments made on the lagging-strand template.
Describe the problem created by a moving replication fork
when the end of a chromosome approaches, while leading strand can be replicated all the way to the end, lagging strand cannot.
explain how DNA topoisomerases solve the moving replication fork problem
- in bacteria they have circular DNA molecules as chromosomes.
- Eukaryotes, DNA topoisomerase adds long repetitive nucleotide sequences to the ends of every chromosomes.
Explain how DNA polymerase contributes to the accuracy of DNA replication.
DNA repair polymerases (I and III) removes the RNA, proofreads, and synthesizes DNA
Thermal collisions
- chemical changes in DNA.
- purine bases (A&G) will be lost by a spontaneous reaction called Depurination.
Deamination
loss of amino group from a cytosine in DNA to produce the base uracil
UV radiation dna damage
cause covalent linkage between two adjacent pyrimidine bases, forming thymine dimer.
cell metabolism dna damage
incorrect base-pairing during replication or to deletion of one or more nucleotide pairs
List the three main steps involved in repairing damage that affects only one strand of the DNA double helix
Step 1: The damaged DNA is recognized and removed.
Step 2: A repair DNA polymerase binds to the 3’-hydroxl end of the cute DNA strand. the enzyme fills in the gap
Step 3: This nick in the helix is sealed by DNA ligase.
Explain how the mismatch repair system recognizes and corrects replication errors.
- removed a portion of the DNA strand containing the error, and then resynthesize the missing DNA
Non-homologous end joining
specialized group of enzymes that “clean” the broken ends and rejoin them by DNA ligation
Homologous recombination
specific nuclease chews back the 5’ ends of the two broken strands at the break. Then, with the help of specialized enzymes one of the broken 3’ ends “invades” the unbroken homologous DNA duplex and searches for a complementary sequence through base pairing.
where are the 3 places that require tons of atp
- dna helicase
- ## sliding clamp
