Download Answers for Worksheet 4.1-4.2 - Background to RNA transcription

RNA background and
transcription answers.
Supplemental Instruction
Iowa State University
Leader:
Course:
Instructor:
Date:
Matt C.
Biol/Gen 313
Dr. Myers & Dr. Vollbrecht
01/26/2017
Introduction: The answers here correspond to the first and second set of questions on the fourth
worksheet.
Concepts
1. RNA background.
2. RNA transcription.
Material
1. RNA background.
In this section, we’ll discuss the types of RNA and differences between RNA and DNA.
1. Name the three most significant classes of RNA and what they’re used for.
Messenger RNA – mRNA carries genetic information to the ribosomes. It provides
the template for translation / protein synthesis.
Ribosomal RNA – rRNA is catalytic RNA – a ribozyme – that makes up a large
component of the ribosome. This rRNA catalyzes the addition of amino acids to a
peptide chain.
Transfer RNA – tRNAs make a cloverleaf structure and carry amino acids to
ribosomes. The tRNAs all have anticodons that match up to codons on the mRNA.
We’ll be talking about codons/anticodons and protein translation more later.
2. The smaller subclasses of RNA all act like a single one of the major classes. Which?
How so?
The subclasses are most comparable to tRNA. Where mRNA’s job is to carry genetic
information and rRNA is meant to catalyze reactions, tRNA is meant to match up to a
certain sequence. All of the smaller subclasses complete their roles by matching up to
certain DNA sequences. They are involved in different roles, but those different jobs
are completed by proteins that associate with the small RNA pieces. I’ll include a
longer discussion of micro-, small interfering- and CRISPR RNAs in the fifth
worksheet.
3. Why not just use DNA in the place of mRNA? Why don’t your cells use “mDNA?”
This is because DNA is really stable and it’s a convenient differentiation method. For
the first reason, you don’t always want mRNA to keep floating around. It’s better for
the mRNA to have a limited lifespan in the cell so you can better control what
proteins are being synthesized.
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The other reason is that it’s simpler if proteins meant to target the genome, not the
supporting nucleic acids, have a chemical difference to take advantage of (the lack of
a hydroxyl on DNA).
2. RNA transcription.
Just like DNA replication, you’ll have a diagram and a set of proteins you’ll have to
remember here. Since the proteins involved in RNA transcription are simpler, though,
we’re also adding on the need to understand translation.
1. What do promoters do?
Promoters mark where a gene starts for transcription. The transcription proteins will
bind onto the promoter sequence(s) and use those sequences to guide the protein to
the start site: the +1 site. In bacteria, there are two specific promoter sequences; the
-10 and -35 sequences and those are what the sigma factor binds to. The +1, -10, and
-35 notation indicates where the site is in reference to the start of the transcribed gene
sequence. Eukaryotes have their own promoters and they’re more complex. We’ll
discuss these more later.
2. Here’s a diagram of an RNA-coding double-stranded DNA sequence from bacteria.
Label the important parts of it. Include as much information as you can.
Downstream
-35 Site -10 Site
Non-template strand
Template strand
Upstream
5’
3’
3’
5’
+1 Site
Terminator
mRNA-coding region
Promoter
3. What parts of the above diagram are transcribed? What does the mRNA look like?
The mRNA-coding region is the portion that is transcribed, including the terminator.
I’ll include here that the resulting mRNA is not going to be translated in its entirety.
Even in prokaryotes, there are regions upstream and downstream from the gene
sequence that are not-transcribed. These are the 5’- and 3’-untranslated regions (5’- or
3’-UTR: 3’ is going towards former terminator and 5’ is going towards where the +1
site was).
4. What are consensus sequences? How’re they used in bacterial promoters?
Consensus sequences are sequences in the bases of DNA that are conserved between
many species. This shows an evolutionary relationship and also allows organisms to
simplify their translational control machinery. The -10 and -35 sequences are
examples of consensus sequences in bacteria. The -10 consensus sequence is
TATAAT and the -35 is TTGACA according to your book.
5. What are the differences between an mRNA-coding region in bacterial DNA and one
in eukaryotic DNA?
You can point out significant differences in the structures of their promoters, but the
most interesting difference is the presence of introns and exons in DNA. Bacteria
don’t need to process their mRNA after synthesis, but eukaryotes do. Especially to
remove intron sequences.
6. What would happen to a bacterium if a mutation occurred which prevented its sigma
factor from binding to the RNA polymerase complex? What would happen if a
mutation prevented the sigma factor from releasing from the holoenzyme complex?
Sigma factor binding allows specificity. RNA polymerase can act without sigma
factor, but it will bind randomly along the chromosome and will just synthesize until
it hits a termination point. This would result in a lot of wasted nucleotides and energy.
If the sigma factor remains bound to the rest of the holoenzyme, it will slow down the
polymerase activity. RNA polymerase only needs the sigma factor to bind and get
through adding the first few nucleotides. After that point sigma factor usually releases
and the rest of the RNA polymerase complex can proceed much quicker.
7. Explain rho-independent and rho-dependent termination. What does the formation of
an RNA hairpin do? Which termination method relies on A/T binding?
This we’re going to talk through in Tuesday’s session. It’s a rather nasty process.