CH 7 Flashcards
Do plasmids and chromosomes mix?
the two forms of DNA do not mingle
Note: Plasmid: A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently.
Codes for one protein
monocistronic
codes for three proteins
polycistronic
a group of genes that are regulated as a unit
regulon
In a bacterial nucleoid what does a nick made in a single strand do to the nucleiod strand
supercoiling relaxes in the nicked strand
- relaxes only one loop
enzymes involved with the topology (geometric properties) of dna
- topoisomerase 1
- topoisomerase 2
what does type one topoisomerase do?
Topoisomerase I relaxes a negatively supercoiled DNA molecule by introducing a single-strand nick. Start with 5 and
end up with four negative supercoils
- Does not require energy
what does type two topoisomerase do?
makes a double-strand break and makes negative super coiling
- requires energy (ATP)
- Ex: DNA gyrase
what antibiotic attacks dna gyrases
quinolones, kill bacteria by targeting dna gyrase
cost: can produce connective tissue damage
What is a nucleoid
a nucleoid consists of DNA arranged in loops w boundaries held up by histone-like anchoring proteins
what is a negative supercoil
Releases strain of underwound dna
what is a positive super coil
releases strain of overwound dna
what is semiconservative replication
- A replication bubble with two replication forks.
- Replication is called “semiconservative” because one parental strand is conserved and inherited by each daughter cell genome. - It is called “bidirectional” because it begins at a fixed origin and progresses in opposite directions.
Where does DNAATP bind to
origin of replication (oriC)
what are the two primary DNA polymerases in bacteria
DNA polymerase 1 and 3
What is DNA polymerase 3
Main polymerase in bacteria
gap filling dna polymerase in bacteria
DNA polymerase 1
what are okazaki fragments
Relatively short fragment of DNA synthesized on the lagging strand during DNA replication
purpose of dna binding proteins
keep dna from hybridizing
DNA replication occurs in what direction
5’ to 3’
what is the purpose of helicase in dna replication
separates the strands of the double helix
purpose of single stranded binding proteins in dna replication
stabilizing single-stranded regions
Purpose of DNA gyrase in dna replication
keeps the dna from supercoiling
Purpose of DNA polymerase 1 in dna replication
functions to fill DNA gaps that arise during DNA replication, repair, and recombination
Purpose of primase in dna replication
synthesizing short RNA sequences that are complementary to a single-stranded piece of DNA, which serves as its template.
purpose of primer
serves to prime and lay a foundation for DNA polymerase
continuous synthesis of DNA occurs in what direction?
3’ to 5’ (leading strand)
discontinuous strand occurs in what direction
5’ to 3’ called the lagging strand which is completed in segments called okazaki fragments
purpose of DNA polymerase 3 in lagging strand
adds Okazaki fragments to the primer of lagging strand
Purpose of DNA ligase in DNA replication
glues fragments in dna replication together
DNA replication in prokaryotes video:
https://www.youtube.com/watch?v=HSoKeKV5ecs
Removing the RNA primer
The 3′-to-5′ exonuclease activity of Pol I or RNase H cleaves the RNA primer
What is the role of exonuclease?
act as proof-readers during DNA polymerisation in DNA replication, to remove unusual DNA structures that arise from problems with DNA replication fork progression, and they can be directly involved in repairing damaged DNA.
Purpose of XerCD in terminating replication of the chromosome
type 2 topoisomerases that pass linked chromosomes through each other to forme a catenane
Purpose of FtsZ
key in septum formation for chromosome segregation which leads to cell division
what is SimA
a protein that binds to FtsZ which prevents septum fromation
two categories of plasmids
- high copy number plasmids- 50 to 700 copies of plasmid (lower molecular weight)
- low copy number plasmid- 1 to 3 copies
what type of plasmids are non-conjugated
high ccopy number
what type of plasmids are conjugated
low copy number
how many basepairs per gene in plasmids
1000
PBR322 is a plasmid that is the basis for what?
used in genetic engineering
Plasmids reproduce by
rolling circle replication
- some viruses use rolling circle to make concatimores to make opies of viruses
purpose of repA in rolling circle replication
binds to the origin of replication (ori)
- nicks one strand of the dna and holds on to the 5’ so that the 3’ end can be used as a primer
purpose of DNA polymerase 3 in rolling circle replication
binds to 3’ end primer to begin replication
rolling circle replication video:
https://www.youtube.com/watch?v=ZDqsojQ8A5k
what is the function of ParM in plasmids?
ParM is a prokaryotic actin carrier which provides the force to drive copies of the plasmids to opposite ends of rod shaped bacteria before cytokinesis
how was the ParM filament visualized
ParM filament was seen by combined phase-contrast and immunofluorescence microscopy
Key difference between prokaryote and eukaryote cells when it comes to genome structure
Prokaryotes: introns
Eukaryotes: no introns
How many RNA polymerases do Bacteria have
one (RNAP)
Eukaryotes have how many RNA polymerases
three
- one for transfer RNA
- RNA polymerase 2 (mRNA)
- RNA polymerase 3
Archea and eukaryotes share what when it comes to genome structure
- the TATA binding protein
- TFB
Do bacterial antibiotics work on archea? and are there any pathogenic archea
No they do not
- there are no pathogenic archea
Two ways to protect DNA
- telomeres
- looping of DNA
What E. coli pathogen strain kill humans
E. coli 0157
What are the three basic methods for DNA sequencing
- Sanger sequencing
- pyro sequencing
- illumina
compare and contrast between pyro and illumina sequenccing
- they both involve synthesis
- pyro uses fire flies
- illumina uses floreccent lable
what organism affects obesity in a positive way (makes people less obese)
christensenella
what are gnotobiotic mice
germ free mice
tow biological ways that obesity can be affected
- herpes
- gut-microbiome
Definition of metagenomics
metagenomics studies the collection of different organisms’ genomes within a sample
definition of genomics
Genomics studies the genome of a single organism
