Download POGIL 6 Worksheet EukGR Data Set 2

Eukaryotic Gene Regulation: Data Set 2
Fig. 3
Bacterial DNA (electron micrograph)
Fig. 1
Bacterial
Basal
Transcription
Levels
Eukaryotic DNA (electron micrograph):
All promoters analyzed have the
same DNA sequence
Fig. 2
Eukaryotic
Basal
Transcription
Levels
Fig. 4
Which of these hypotheses best fits and
explains the data shown?
1. 
2. 
3. 
4. 
All promoters have the same level of basal transcription
Some physical interaction with the DNA disrupts
transcription at some promoters in eukaryotes
Prokaryotes have no proteins that touch DNA
Eukaryotes have more promoters overall which causes
them to occasionally wrap around random proteins in the
nucleus
Histones
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Histones are proteins that help pack the DNA of
eukaryotes. This compressed the size of the huge
chromosomes and also helps protect DNA from
damage.
Since the phosphodiester backbone of DNA is
negatively charged, histones have positively charged
R-groups to interact tightly with DNA.
Histones: Enzymatic unpacking
Histone De-Acetylase:
-Removes a negatively charged acetyl group
-Makes histone more positively charged
-Produces tightly packed DNA
Histone Acetyl Transferase:
-Adds a negatively charged acetyl group
-Makes histone more negatively charged
-Produces unpacked DNA
Eukaryotic Gene Regulation: Data Set 3
Single stranded DNA from a gene:
mRNA from the same gene:
We can isolate RNA and DNA from cells, separate the DNA strands, and
allow them to form hybrid double-stranded molecules
From a prokaryote gene:
From a eukaryote gene:
Which of these hypotheses fits the data shown?
1. 
2. 
3. 
4. 
In eukaryotes, the mRNA is elongated compared to the
DNA from which it was transcribed
In eukaryotes, interior regions of the mRNA have been
removed
In eukaryotes, something has been added to the ends of
the mRNA that is not found in the corresponding DNA
sequence
In eukaryotes, interior regions of the mRNA have been
removed and something has been added to the end of the
mRNA
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Introns must be removed from RNA transcripts.!
Splicing
Intron 1!
The final mRNA has an Open
Reading Frame that looks similar
to what we would see in a
prokaryotic mRNA. The original
eukaryotic mRNA will not have a
full ORF. The codon frame is only
correct after splicing.
Intron 2!
3!!
DNA!
5!!
Promoter!
Primary RNA transcript!
Spliced transcript!
Exon 2!
Exon 1!
5!!
3!!
3!!
5!!
Small RNA molecules called small nuclear ribosomal
proteins (snRPs) come together to form a complex ribozyme
called the spliceosome.
Primary
RNA!
5!!
Exon 1!
This ribozyme finds special binding sites on eukaryotic
mRNA and uses those binding sites to cut out intron DNA,
leaving a final message.
Exon 3!
5!!
Spliceosome!
snRPs!
Intron! A!
A!
3!!
Exon 2!
3!!
The final processed mRNA has two protection molecules
added:
-On the 5 end, a special cap
-On the 3 end, a long tail addition of adenosine (A)
nucleotides
5!!
3!!
5!!
A!
5!! 3!!
Excised
intron!
A!
Both cap and tail help prevent mRNA degradation in the
cytoplasm.
Mature mRNA!
5!!
Exon 1!
3!!
Exon 2!
Multiple protein types
from the same gene?
Proteins can adjust spliceosome function so that it
does not always use the same binding sites.
This can change the final mRNA sequence in
blocks , which changes the final protein primary
structure (and also the secondary, tertiary and
quarternary structure).
This is called alternative splicing .
1
2
3
Exon
4
5
6
Intron
Protein found in Neurons
(each oval is a small region of protein):
A protein from the exact same gene, but
this variant is found in Skin Cells
Eukaryotic Gene Regulation: Data Set 4
Protein-coding mRNA
region for Gene Z
Amino-acid primary
Sequence for Gene Z
= Lysine
Life span of
the mutant
protein
(Life span of
non-mutant
protein Z)
Location of amino-acid-changing mutation
How to read this graph:
If you made a mutation in the 3rd amino acid (blue), then the lifespan of the mutant protein would
be just a little bit shorter on average than the non-mutant protein Z.
Which of these hypotheses fits the data shown?
1.  Lysines live longer than other amino-acids
2.  Lysine amino-acids are somehow important for
regulating protein life-spans
3.  Proteins can have different life spans in the cell
4.  Mutations in any amino-acid cause massive
changes in protein life-spans
Eukaryotic Gene Regulation:
Post-translational Ubiquitination
• 
• 
• 
• 
The small protein Ubiquitin (Ub) is common in most cells.
Special enzymes called Ubiquitin Ligases add these
small Ubiquitin proteins to enzymes or structural proteins
that are damaged or need to be degraded rapidly. This
addition is done by binding Ub to lysine R-groups
Additional Ub molecules can be added to form a
Ub-chain hanging from the protein to be recycled.
Ub-tagged proteins are degraded at the proteasome.
An example with the protein cyclin :
The Proteasome:
Using Ubiquitin-tagging to destroy
damaged or unwanted proteins
• 
• 
• 
• 
Regulatory proteins bring Ub-tagged proteins to
the proteasome
The barrel-shaped proteasome opens up and
allows the protein to enter
Peptide bonds are catalytically hydrolyzed
The amino-acids and Ubiquitin proteins are
recycled.
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A single Ubiquitin protein