02/11/2025 Flashcards
which two enzymes in DNA replication of bacteria have exonuclease activity? Do any have endo?
DNA pol I has a 5’-3’ exonuclease activity to remove primers
DNA pol III has a 3’-5’ exonuclease site to remove errors
none of these have an endonuclease function
true or false
to remove errors in DNA replication of bacterial DNA, DNA pol I removes it with an endonuclease activity
false
DNA pol I removes primers with EXONUCLEASE activity
to remove errors, DNA pol III removes it with 3’-5’ EXOnuclease activity
what are the three main reasons that DNA replication is more complex in eukaryotes vs prokaryotes
eukaryotes have
- larger linear chromosomes
-tight packaging within nucleosomes
- more complicated cell cycle regulation
why is it a problem that eukaryotes have larger linear chromosomes
- more DNA to replicate
- the linear form requires a stopping point and telomeres pose issues of shortening
why is it a problem that eukaryotes have tight packaging within nucleosomes
it makes DNA replication slower
why is it a problem that eukaryotes have more complicated cell cycle regulation
they are more time dependent on the different cycle phases
bacteria do not depend on these phases as much and often times will rapid fire replication so they can divide and grow as much as possible
what is the minimal amount of origins of replication are required per chromosome
one
Since humans have 46 chromosomes, then the most minimal number of origins of replication we must have is 46
true
why do eukaryotes have multiple origins of replications
they have longer chromosomes
How are saccharomyces cerevisaie similar to bacteria? Why is this important
these are very simple eukaryotes and have a similar origin of replication.
The main idea is that organisms with simpler construction are more similar to bacteria while complex organisms are different
in terms of DNA replication between prokaryotes and eukaryotes, how are they similar
they both have a replication complex that is formed at the origin
it involves the use of helicase, gyrase, and is bidirectional
in terms of polymerases, how do eukaryotes and prokaryotes compare
eukaryotes have more types of polymerases
𝛼
𝛿
𝜀
𝛾
what is the purpose of 𝛼 𝛿 𝜀
they synthesize the nuclear DNA
what is the purpose of 𝛾 and why do we care
𝛾 is used to synthesize mitochondrial DNA which follows a bacterial model
what is the primary function of DNA pol 𝛼? How is this different from primase?
DNA pol 𝛼 creates a HYBRID primer of RNA and DNA rather than just RNA
it also undergoes polymerase switching with the next polymerase
what is polymerase switching? does it occur in bacteria
it is when the 𝛼 polymerase is switched to 𝛿 and 𝜀 for synthesizing the longer portion of DNA
what is the purpose of flap endonuclease ? How is this different from pol I
DNA pol 𝛿 runs into the fragment of the prior fragment and will push the primer into a flap
ANOTHER enzyme, flap endonuclease will remove the primer through internal cuts but it has no polymerase activity to synthesize the new DNA
is there a parallel of DNA pol I in eukaryotic DNA replication?
no, DNA pol 𝛿 doesn’t have the exonuclease activity that DNA pol I has and flap endonuclease doesn’t have the polymerase activity of pol I
what fuses the okazaki fragments in both eukaryotes and prokaryotes
ligase
what is a telomere
repetitive DNA sequences that are species specific at the end of chromosomes and they have a 3’ overhang
what features of DNA pose problems at telomeres
DNA pol III can only synthesize in the 5-3’ direction and cannot initiate synthesis without a primer, at the 3’ end the DNA runs out of space to synthesize a new primer and DNA is lost
why is it a problem that telomeres shorten?
With every replication cycle, we lose DNA. This occurs naturally in all cells until the cells can no longer replicate and divide, which results in apoptosis
What resolves the issue of telomere shortening?
Stem cells can replace dying cells
How do stem cells not shorten
they add DNA sequences to the ends of telomeres with telomerase
what are the features of telomerase
it contains the protein “reverse transcriptase) and an RNA template that is complimentary to the 3’ overhang
how does reverse transcriptase work?
it uses an RNA template to make DNA
what is the goal of reverse transcriptase and telomerase
it lengthens the 3’ overhang by adding new repetitive telomeric sequences and this allows a new primer to be added and DNA can be synthesized regularly to complete the replication
Describe the function of telomerase
which cells have the gene for telomerase? which ones can use it?
all cells gace the genes for telomerase but only stem cells and cancer cells can use it
when comparing lagging strand synthesis of eukaryotes to prokaryotes, okazaki fragments are also removed by a polymerase enzyme like DNA pol I
true or false
false, flap endonuclease performs this function. The polymerase can only synthesize it
what is the promoter
it is the site for RNA polymerase binding and it signals the beginning of transcription
is the promoter itself transcribed
no, it is not transcribed and RNA is not synthesized here either, it is synthesized down stream
what are regulatory sequences
they are sequences where regulatory proteins bind to and influence gene expression (tell you to turn it on or off)
what is the role of the terminator sequence in in transcription
it signals the end of transcription
Do the first and last RNA bases made in mRNA code for amino acids?
no, these are untranslated regions
if we didnt have the 5’ UTR and 3’ UTR what would occur
we would not be able to synthesize the polypeptiden
what is the ribosome binding site? where is it?
it is the site where the ribosome will bind on the mRNA, it is ahead of the start codon where translation will begin
what is a codon
it is a three nucleotide sequence in mRNA that codes for an amino aci
in transcription, what is the template/antisense strand
it is the DNA strand that the RNA pol will read and transcribe, it is in the opposite direction of the synthesized strand and is complementary
in transcription, what is the coding/nontemplate/ sense strand
it is the DNA strand that is not transcribed. It is identical to the RNA transcript with the exception of (T=U) and it is in the same direction
which mRNA sequences direct translation
ribosomal binding sites and codons
what are transcription factors
they recognize the promoter and regulatory sequences to control transcription
what are the three stages of transcription
initiation, elongation, termination
what types of sequences give RNA transcripts that are not translated
non-structural genes
what are some examples of RNA transcripts that become parts of protein subunits
spliceosomes, ribosomes, signal recognition particles, telomerase
what is mRNA
it is messenger rna that encodes for amino acids in translation
what is t RNA
it is transfer RNA, it carries amino acids to the ribosome for growing polypeptides
what is rRNA
it is ribsomal RNA and makes up a mahor component of the ribosomal complex that is essential for protein synthesis with mRNA as a template
