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BIOL 3335 Chapter 2
Terms in this set (80)
predominant form of bacterial chromosome
conformation forms of a bacterial chromosome
B, A, Z
length of a bacterial cell
15 - 30 mg/ml
first level of condensation
what controls supercoiling?
how many types of topoisomerases are there?
topoisomerase I characteristics
(1) relaxes supercoiling, involves a single-strand nick
(2) does not require energy
topoisomerase II characteristics
(1) negative supercoiling
(2) dsDNA passes through a double strand break
(3) requires energy
(1) smallest protein in the cell
(2) positively charged
nucleoid structure theory
dynamic (non-static) structure with ribosomes on the outside, no region of DNA appears to be permanently in one place
repetitive extragenic elements (REP)
(1) 38 base pair repeats
(2) 500 - 1000 copies per genome
(3) repeats located between genes in an operon or between operons
purpose of REPs
participate in chromosomal condensation and organization (bind DNA polymerase I and DNA gyrase)
5 DNPs in E. coli
(1) PolA (repair)
(2) DinA (replication)
DNA synthesis occurs in what direction?
5' to 3'
what is required for DNA synthesis
3' to 5' exonuclease function
5' to 3' exonuclease function
remove stuff in the way
Pol I has what exonuclease activity?
3' to 5' and 5' to 3'
Pol II and III have what exonuclease activity?
3' to 5'
do bacteria want DNA to be AT or CG rich?
how many base pairs are DNA primers?
11 base pairs
what synthesizes both strands?
what is required at the replication fork to synthesize both strands?
DNA polymerase III dimer
(1) strand separation by a helicase hexamer (DnaB)
(2) loading factor brings helicase to origin
(3) helicase encircles one strand of DNA
(4) when DNP III loaded, unwinding activity of helicase 10-fold stimulated
DnaB creates hairpin in single stranded DNA
when is DnaG recruied?
as needed (not part of replication fork)
incorporation of an incorrect base noted by 3' to 5' exonuclease proofreading function
what is the positive regulator of initiation?
what loads DnaB?
strand separation promoted by DnaA
DnaA binds to this which is localized to the cell poles and septum?
Converts DnaA-ATP(active) to DnaA-ADP (inactive), which prevents early reinitiation.
A negative regulator that binds to origi and prevents reinitiation. It also binds the origin to the membrane.
A DNA-binding protein that promotes a DnaA complex. Timing not understood.
Binds tightly to hemimethylated DNA, which is present just after replication begins. Also prevents methylation of these sites for at least 13 minutes.
Contains 11 methylation sites.
Located at the center of the cell. After replication, they move to cell poles.
Replication of one chromosome takes?
Allows counterclockwise replication, but blocks clockwise replication.
Allows clockwise replication but blocks counterclockwise replication.
Blocks the helicase of replicating DNA
Tus, terminus utilization substance
Makes all three RNAs (tRNA, rRNA, and mRNA). This is not true in eukaryotes.
One RNA polymerase (RNP)
RNP contains what 4 subunits?
alpha, beta, beta prime, sigma
What is the core RNP that binds randomly to DNA with low affinity.
alpha 2, beta, beta prime
What subunit in the Holoenzyme allows for specific binding to promoter sites?
Known as the housekeeping sigma which transcribes most genes?
has the catalytic site for RNA synthesis, and therefore contains binding sites for substrates and products.
Common antibiotic that interfers with the Beta subunit.
Binds the DNA template.
Used to make the mRNA.
anti-sense template strand (- strand)
not transcribed but also contains the same sequence as the mRNA.
Coding strand (+ strand)
The -10 is known as the
RNP makes simultaneous contact with bases in the -10 and -35 regions, via protein-nucleic acid interactions in the major groove. The complex is known as
closed promoter complex
Why is the closed promoter complex called that?
because the strands have not yet separated.
E. Coli contains seven sigma factors. All are homologous to each other except for this which is radically different.
interacts with DNA, upstream from the -35 region. It can also interact with transcriptional activator proteins.
Many regulatory factors interact with RNP at the promoter region. They bind to either of these subunits.
alpha or sigma subunits
Transcription usually starts before the
structural gene (the coding region)
The non-coding region of the mRNA contains sites for
is released after about 10 nucleotides, and free to bind another molecule of core.
Transcription occurs at this many nucleotides per second with regions of pausing, where the RNA forms a hairpin and interacts with RNP
3 steps of termination
cessation of elongation, release of transcript from (DNA-RNA-RNP_, and dissociation of RNP-DNA complex
2 types of termination
Rho-dependent and Rho-independent
what termination Involves a GC-rich stem-loop and a stretch of 4-8 uridines.
Stem loop causes
weak rU-dA hybrid causes
release of the DNA-RNA hybrid.
what kind of Termination occurs at strong pause sites
rRNA is what % all RNA
mRNA is what % of all RNA
tRNA is what % of all RNA
tRNA and rRNA
What factors increase stability in RNA?
Localization in ribosomes, secondary structure, and perhaps modified bases
Degradation occurs in the, with exception of exonucleases
5' to 3' direction
Bacterial mRNA contain these which appear to stimulate degradation.
Poly (A) tails
What are the 7 rRNA transcription units with the structure?
5' leader, 16S rRNA, spacer, 23S rRNA, 5s rRNA, trailer - 3'
Involves initial cleavages, trimming to get precise 5' and 3' ends, addition of extra nucleotides to termini, and modification of bases
degrades RNA in an RNA-DNA hybrid
recognizes a strucure not sequence, endonucleolytic enzyme for maturation of tRNAs.
Average mRNA has a half-life of?
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