Bacterial replication, transcription, translation Flashcards
Prokaryotic genomes
They have fewer chromosomes than eukaryotes and are usually circular
they also include plasmids - which are much smaller than chromosomes
what is the size of human chromosomes
47,000-250,000 kb (47-250 million bp)
How do prokaryotic genomes fit in the cell?
supercoiling
What is supercoiling?
main circular chromosomes
They wrap the DNA around histone-like proteins, and twists the DNA to be compact with the help of Topoisomerase II and I
negative supercoiling compacts the genome another 100x
What does Topoisomerase II do?
makes a negative supercoil
and it cuts double strand of DNA helix and then reseals them
What does Topoisomerase I do?
it makes a positive superocoil and converts the DNA back to its original state
it cuts a single strand of the DNA helix and reseals the break, this helps relieve tension
what is monocistronic
one promoter encodes one gene
what is polycistronic
one promoter encodes multiple genes
what are the steps of bacterial replication
- when the cell is ready for replication a replication initiation factor (DnaA) binds to the origin and a replication bubble opens
- then the helicase unwinds DNA and the single stranded DNA-binding proteins (ssDNA-binding proteins) bind to the DNA. replication forks progress in opposite directions. gyrase releases supercoil
- then DNA polymerase III extends the primers and the replication forks progress in opposite directions
- Leading and lagging strands form and DNA polymerase III has proof reading capacity
- DNA polymerase I removes primers and replaces them with DNA
Ligase repairs the nicks
how many origins and terminus are there in a bacterial chromosomes
one origin and one terminus
What is gyrase and what does it do?
Gyrase (topoisomerase) cuts the DNA strands and allow it to free rotate
where does replication take place in prokaryotes vs eukaryotes?
replication occurs in the cytoplasm for prokaryotes
and it occurs in the nucleus for eukaryotes
What is catenane?
a unique problem for circular genomes where DNA replication results in a catenane of linked rings
this is where topoisomerase comes into play
it breaks and re-joins the strands resolving the link
what are plasmids and what are the advantages?
they are always circular and are much smaller than bacterial chromosomes
they arent normally required by the cell but they can have some advantages like
- antibiotic resistance
- synthesis of antibiotics
- nitrogen fixation
- resistance to toxic metals
- pathogenesis
how do plasmids replicate?
they replicate independently from chromosomes and it is happening all the time
they do rolling circle replication, Rep A binds to a section of the plasmid’s double stranded DNA by nicking one of the strands and hold on to the 5’ prime end to allow 3’ prime end to act as a host for DNA polymerase and then it recruits a helicase to unwind the DNA and it becomes a single strand the two ends of the nick strand are rejoined by the rep A and the DNA ligase seals the nick in the single strand
the single strand DNA can now be replicated and the region of DNA becomes looped allowing RNA polymerase access to the DNA to form a primer and host DNA polymerase uses the primer as a synthesis of DNA
why is having low levels of plasmid a disadvantage
because if the cell divides then you may be left with a daughter cell that did not receive the plasmid
what is the structure of bacteria genes and when are they functional?
promoter –> RBS (ribosome binding site) –> ATG –> coding –> stop codon –> terminator
during transcription only the promoter and terminator are functional (RNA polymerase reads the terminator as the ending signal and the promoter as the beginning signal)
during translation only the RBS, ATG, coding, and stop codon are functional
when does transcription start?
After the promoter (+1)
What does RNA polymerases do?
It carries out transcription y making RNA transcripts from DNA template strands
What are sigma factors and where do they bind?
they direct RNA polymerase to specific promoters
sigma factors bind to
-10 element
-35 element
what are the phases that don’t change?
conserve, you can take the most conserve nucleotides and make a consensus sequence
what are the stages of transcription?
3 stages
- Initiation
- RNA polymerase holoenyzme binds DNA and scans for promoter - elongation
- sigma factor falls off, and the RNA is extended within a transcription bubble, gyrase relaxes the supercoiling caused by unzipping the DNA - termination
- RNA polymerase and the transcript fall off
Which is the complimentary stand and which is the template strand during transcription
the top strand is complimentary and the bottom is the template strand
mRNA is made using the lower strand as a template
what are the types of RNA?
- mRNA (messenger RNA)
- rRNA (ribosomal RNA)
- tRNA (transfer RNA)
what do mRNA do?
they encode proteins and this all happens in the cytoplasm
what do rRNAs do?
they form ribosomes and is catalytic (structural, does not get translated, is apart of ribosome)
ribosomes are made up of proteins and RNA and they have no membrane
what is ribozyme?
a peptidyltransferase that catalyzes a reaction
a catalytic RNA
what do tRNA do?
they shuttle amino acids for translation
they are each bond to an amino acid and they bring it to the RBS
they have an anticodon loop and acceptor end
what are the steps for bacterial translation?
- Ribosome binds to RBS
- Amino acids are brought by tRNA and fMet
- Translation stop when the stop codon shows up
What occurs simultaneously at the same time?
Transcription and translation because there is no nucleus separating them
once transcription ends the 5’ end of the RNA comes off and the ribosome jumps on the RBS and it reads the RNA 5’ to 3’
