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bio_exam_2_study_guide_2.docx-Study guide for metabolic regulation, citric
Page 33
Sources of DNA damage:
Ionizing radiation: x-rays, radon
single and double strand DNA breaks
UV radiation: sun exposure
bulkiness distrupts structure and replication
Chemicals: chemotherapy
damaged bases
Reactive oxygen species: normal cell metabolism
oxidative damage
In prokaryotes, transcription occurs in the cytoplasm. In eukaryotes, transcription
occurs in the nucleus. Both use promoters during gene expression; Gene expression
is controlled by the use of bound regulatory proteins to the regulatory region of the
gene or operon.
The transcription start site is the same, at the 1+ nucleotide.
Sigma factor: promoter recognition, positions holoenzyme to initiate transcription:
binds to -10 and -35 regions of promoter, dissociates from other subunits after RNA
synthesis begins
4. Compare and contrast gene structure and gene expression in prokaryotes and
eukaryotes. This is a great “synthesis exercise” that requires combined understanding of
Dr. Kunkel’s lectures and information from Dr. Major’s lectures on eukaryotic gene
structure (so some of this synthesis will have to occur at a later time). This tests your
overall understand of gene structure and gene expression. Key terms: Location of
transcription (nucleus vs cytoplasm), promoter, regulatory region, transcription start site,
ORF, intron, exon, operon, polycistronic mRNA, poly adenylation, primary transcript,
processed or final mRNA, RNA splicing, export of mRNA,

Page 34
In prokaryotes:
-small genome
-single chromosome
-single origin of replication
-circular chromosome
-all in cytoplasm
In eurkaryotes:
-large genome
-many chromoseomes
-multiple origins of replications
-linear chromosome

Page 35
5. Compare and contrast the events that take place at a DNA replication bubble and a
transcription bubble. Diagram both, in detail, and explain the processes that occur at both.
• Notice the similarities and differences between the direction of polymerization •
Identify the template strands, label 5’ and 3’ ends
• List and describe enzymes involved:
• Compare and contrast how each process is initiated, terminated, regulated.
DNA Replication Bubble
Transcription Bubble
While polymerization is 5’ to 3’, you have
the lagging and leading strands going in
both directions of the replication bubble.
Both DNA strands can serve as templates.
Initiated by the binding of primers, which
alert DNA pol where to start replication
Elongated by DNA pol (a little more
complicated for Okazaki fragments, with
ligase activity)
Terminated by either joining the strands
(in circular DNA) or with telomerase (in
linear DNA)
Typically, there’s only one RNA being
synthetized in the replication bubble from
one template DNA strand.
Initiated by RNA polymerase and protein
factors; doesn’t need a primer to tell RNA
pol where to start (promoter does that)
Elongated by RNA polymerase
Terminated by hairpin loop or rho protein

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