Download Introns and mutations

Welcome to
Introduction to Bioinformatics
Wednesday, 25 January
Introduction to Molecular Biology
Part 2: DNA to protein
• Coming attractions!
• Significance
• Palindromes (SQ4)
• Why introns? (SQ8)
• Types of mutation (SQ12)
Study Question 8
Why do introns exist?
I do not understand why introns
would even exist.
I dont understand why the
information for a single element
would be spread out.
Well, they do seem pretty mysterious.
I’ll quickly review what introns and
exons are and then propose an
explanation as to why they might
serve a useful purpose.
Study Question 8
Why do introns exist?
DNA
Transcription
Primary
transcript
(hnRNA)
Transcription is a key step in the
expression of genes, i.e. the chain
of events that convert information
on DNA into cell behavior.
The end product of transcription is
a molecule of RNA corresponding
to a small fraction of the DNA.
Study Question 8
Why do introns exist?
DNA
Transcription
Primary
transcript
(hnRNA)
AAAAAA...AAA
MeG
cap
Poly-A tail
In eukaryotes, the primary transcript
(i.e. the direct RNA product of transcription)
is processed before it is used in translation.
One modification is a special guanosine
placed at the 5’ end of the message.
Another is a string of adenosines placed
at the 3’ end of the message.
Study Question 8
Why do introns exist?
DNA
Transcription
Primary
AAAAAA...AAA
transcript
G cap
Poly-A tail
(hnRNA)
They function in the stability of the message and
in helping ribosomes bind to the RNA’s 5’ end.
Me
However, poly-A tails are much less
important in bacteria and their viruses,
and caps are (to my knowledge) absent.
Since we will be focusing on bacterial viruses,
these structures needn’t concern us now.
Study Question 8
Why do introns exist?
DNA
Transcription
Primary
AAAAAA...AAA
transcript
G cap
Poly-A tail
(hnRNA)
Transcripts are subject to a third modification.
If you looked at the sequence of a transcript,
you would not find anything in one region
to distinguish it from another.
Me
However protein-nucleic acid complexes
in the nucleus of eukaryotic cells recognize
certain sites ( ) in the message.
Study Question 8
Why do introns exist?
Primary
transcript
(hnRNA)
AAAAAA...AAA
MeG
cap
Poly-A tail
Intron
Splicing
Processed
transcript
(mRNA)
Exon
AAAAAA...AAA
These complexes cause some of the RNA to be
cut out, a process called splicing.
RNA that’s cut out is called an intron.
RNA that’s left in is called an exon.
Study Question 8
Why do introns exist?
Primary
transcript
(hnRNA)
AAAAAA...AAA
MeG
cap
Poly-A tail
Splicing
Processed
transcript
(mRNA)
Intron
Exon
AAAAAA...AAA
It is the mature, processed transcript that enters
the cytoplasm and is translated by ribosomes.
Study Question 8
Why do introns exist?
Primary
transcript
(hnRNA)
AAAAAA...AAA
MeG
cap
Poly-A tail
Splicing
Processed
transcript
(mRNA)
…what role
[does] an
intron plays in
translation?
Intron
Exon
AAAAAA...AAA
Where are introns when
translation takes place?
Study Question 8
Why do introns exist?
Primary
transcript
(hnRNA)
AAAAAA...AAA
MeG
cap
Poly-A tail
Splicing
Processed
transcript
(mRNA)
…could you explain…
how a cell's apparatus
distinguishes exon
from intron?
Intron
Exon
AAAAAA...AAA
You could answer this question
the same way you discovered
what is the beginning of a gene.
What would you need to do this?
Study Question 8
Why do introns exist?
That explains what introns are,
but not why they exist.
They’re not necessary… bacteria live
perfectly well even though introns are
very rare in bacteria and their viruses.
In eukaryotes, however, they are very common.
Why?
How do introns contribute to differences
between eukaryotes and prokaryotes?
Study Question 8
Why do introns exist?
Huge differences
amongst bacterial
DNA sequences
Small differences
in morphology
Bacterial sequences change rapidly
in evolutionary time, but major
changes in morphology are rare.
Study Question 8
Why do introns exist?
Small differences
amongst vertebrate
DNA sequences
Large differences
in morphology
http://uncyclopedia.wikia.com/wiki/User:Skinfan13/Upsil
on_Sigma_Sigma/Collaboration/May2010collab
In contrast, eukaryotes can look very different, even
though the sequences of their genes are similar.
The gene sequences of mammals are generally very
similar to each other. They differ in the adjacent
regulatory sequences that control gene expression.
Study Question 8
Why do introns exist?
hormone
responsiveness
protein kinase
Here’s an example of
how introns can contribute
to a drastic change in
phenotype without a drastic
change in sequence.
Suppose that there is a gene
that encodes an enzyme that
responds to a hormone.
Hormone-responsive
protein kinase
The first part of the gene encodes
the part of the protein that
recognizes the hormone, and
the rest encodes the enzyme.
Study Question 8
Why do introns exist?
hormone
responsiveness
protein kinase
Hormone-responsive
protein kinase
DNA binding
DNA-binding protein
Now suppose that there is a second gene, lying
very far away on the chromosome (or even on a different
chromosome). This gene encodes a DNA-binding protein..
Study Question 8
Why do introns exist?
hormone
responsiveness
protein kinase
DNA binding
Since DNA frequently recombines, breaking
and joining with other regions of the
chromosome, the two genes may by
accident find themselves close to each other.
Maybe they’re close enough so
that a single RNA is transcribed
Study Question 8
Why do introns exist?
hormone
responsiveness
protein kinase
DNA binding
Hormone-responsive
DNA-binding protein
Now the splice sites are close enough to produce, after
splicing, an mRNA that would encode a novel protein.
In bacteria, the DNA recombination would have to be
exact. In eukaryotes, somewhere in the vicinity will do.
Study Question 8
Why do introns exist?
hormone
responsiveness
protein kinase
DNA binding
Hormone-responsive
DNA-binding protein
Introns therefore can greatly accelerate the rate of evolution
of proteins of novel functions.
For more on exon shuffling, see
Keren H et al (2010). Nature Rev Genet 11:345-355.
Welcome to
Introduction to Bioinformatics
Wednesday, 25 January
Introduction to Molecular Biology
Part 2: DNA to protein
• Coming attractions!
• Significance
• Palindromes (SQ4)
• Why introns? (SQ8)
• Types of mutation (SQ12)
Study Question 12
Single mutation from AGA
If this question is confusing,
take it apart bit by bit.
Study Question 12
Single mutation from AGA
AGA
arginine
…the AGA codon…
That, at least, might be clear.
Write it down!
Study Question 12
Single mutation from AGA
AGA
arginine
…a single basepair mutation…
What could that mean?
Study Question 12
Single mutation from AGA
AGA
arginine
Basepair? Of course DNA is double
stranded, so a codon in DNA is paired
with complementary nucleotides.
What would be the basepairs
of the AGA codon?
Study Question 12
Single mutation from AGA
AGA
TCT
arginine
Wait, that’s not enough. With double
stranded DNA, you need to show
the direction of each strand.
Where should you put 5’ and where 3’?
Study Question 12
Single mutation from AGA
5’-AGA -3’
3’- TCT -5’
arginine
Yes. Codons (like any other DNA or RNA
sequence) are read 5’ to 3’.
What kind of single basepair
mutations are possible?
What’s an example of a single basepair?
Study Question 12
Single mutation from AGA
5’-AGA -3’
3’- TCT -5’
arginine
That’s one basepair.
What are some possible changes?
Study Question 12
Single mutation from AGA
5’-AGA -3’
3’- TCT -5’
5’-GGA -3’
3’- CCT -5’
arginine
arginine
OK, that’s one possible change.
How many total possible
changes are there?
Note I said “possible”.
A G/A basepair is not possible.
Study Question 12
Single mutation from AGA
AGA
arginine
I’m not going to write basepairs anymore –
you can always imagine them.
Nor am I going to write 5’ and 3’.
Remember, unless specified,
left-to-right is always 5’ to 3’.
Study Question 12
Single mutation from AGA
AGA
arginine
Moving on, what could
“encoding arginine” mean?
I’ll pause so you could
look up what arginine is.
(Google is your friend)
Study Question 12
Single mutation from AGA
AGA
arginine
…an amino acid.
Codons encode amino acids.
Study Question 12
Single mutation from AGA
AGA
arginine
So putting it all together….
…what does the first part
of the question mean?
Study Question 12
Single mutation from AGA
AGA
arginine
Single basepair mutations
in AGA change the codon.
Changing the codon may change
the amino acid that’s encoded.
Which single basepair changes produce
which changes in encoded amino acids?
Study Question 12
Single mutation from AGA
AGA
arginine
What might these terms mean?
They’re likely to refer to the result of the
changes described in the first part of the
question, changes in codons and perhaps
the amino acids they encode.
Start with two we’ve discussed:
hydrophobic and hydrophilic
Study Question 12
Single mutation from AGA
Proteins, Figure 2
Proteins, Figure 1
Look at Figure 2 from the notes on
Proteins. Notice that the amino
acids are arranged in a very similar
manner to the generic amino acid
shown in Figure 1.
There is a constant part that
all amino acids have, and there
is a variable part, labeled R.
Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub
Study Question 12
Single mutation from AGA
Proteins, Figure 2
Proteins, Figure 1
I’ve represented the
constant part as shadowed.
What distinguishes one amino acid
from the others is what’s left.
Consider the amino acids with
hydrophobic R groups. What
generality can you draw from
their chemical constituents?
Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub
Study Question 12
Single mutation from AGA
Proteins, Figure 2
Proteins, Figure 1
Look at them!
Except for methionine, they consist
solely of carbons and hydrogens.
They’re hydrocarbons, like oil.
What about the negatively
charged R groups?
Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub
Study Question 12
Single mutation from AGA
Proteins, Figure 2
Proteins, Figure 1
All the negatively charged
R groups have freeO
carboxylate moieties ( -C-O ),
with negative charges.
-
Positively-charged R groups?
Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub
Study Question 12
Single mutation from AGA
Proteins, Figure 2
Proteins, Figure 1
All positively charged nitrogen
atoms in some form.
Finally, the hydrophilic,
uncharged R groups?
Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub
Study Question 12
Single mutation from AGA
Proteins, Figure 2
Proteins, Figure 1
…a mixed bag, but all of them
have uncharged polar groups,
for example -OH.
Of course, they are different in
other ways: some are large,
some small, some have aromatic
rings, others not.
Each has a different flavor.
Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub
Study Question 12
Single mutation from AGA
AGA
GGA
arginine
???
Now back to the question.
AGA encodes arginine.
Mutations can change the codon.
That might change the encoded amino acid.
That might change the type of amino acid.
We have something that describes the types
of amino acids (left). We need a table that
connects amino acids to their codons.
Study Question 12
Single mutation from AGA
Here's such a table.
You can find
dozens of these on
the web, or use the
genetic table found
on the Resources
& Links section.
First of all, does
AGA indeed
encode arginine?
Learn how to
use this table.
Study Question 12
Single mutation from AGA
How many ways
can AGA be
changed by a single
nucleotide?
Answer this by
counting, and then
figure out how you
could calculate
the number.
How many ways
could a 10-letter
sequence be
changed by a single
nucleotide?
Study Question 12
Single mutation from AGA
…Back to AGA.
Categorize each
change to AGA,
using the labels
given in the
question. How does
the encoded amino
acid change in each
case?
Study Question 12
Single mutation from AGA
(Frequently asked questions)
• If "conservative" is "close enough", how close is that?
A conservative amino acid substitution is one
that should not affect the function of the
protein. However, this is often not easy to
predict. In one context, leucine and isoleucine
might be interchangeable, while in another,
substituting isoleucine for leucine could lead
to an inactive protein.
That isn't a satisfying answer, but it does
reflect our current state of knowledge.
Study Question 12
Single mutation from AGA
(Frequently asked questions)
• If "conservative" is "close enough", how close is that?
• Do we have to learn the 20 amino acids?
If you do, you will.
If the time ever comes when you find
yourself constantly going back to a list
of amino acids and their properties,
you will memorize them without trying.
Until then, the list is always available.
Study Question 12
Single mutation from AGA
(Frequently asked questions)
• If "conservative" is "close enough", how close is that?
• Do we have to learn the 20 amino acids?
• Will we be able to decipher the genetic code of an alien being?
Well now, funny you should ask!
If you go to the Intro to Molecular Biology
topic page, you will find a link to
an investigation called Alien Genetic Code.
Alien Genetic Code
(Coming Attractions!)
CCCCCCCCCCCC
Pro-Pro-Pro-Pro…
Terrestrial
ribosomes
Terrestrial Genetic Code
There you will be given the means
to perform virtual experiments.
Using terrestrial cell extracts and the RNA
CCCCC…, these experiments would produce
poly-proline, according to our genetic code.
Alien Genetic Code
(Coming Attractions!)
CCCCCCCCCCCC
Alien
ribosomes
???
Alien Genetic Code
But using alien cell extracts... who knows?
You can know.
`