Welcome toIntroduction to Bioinformatics
Wednesday, 25 JanuaryIntroduction to Molecular Biology
Part 2: DNA to protein
• Coming attractions!• Significance• Palindromes (SQ4)• Why introns? (SQ8)• Types of mutation (SQ12)
Study Question 8Why 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 8Why do introns exist?
DNA
Primary transcript(hnRNA)
Transcription
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 8Why do introns exist?
AAAAAA...AAA
DNA
Primary transcript(hnRNA) MeG cap Poly-A tail
Transcription
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 8Why do introns exist?
AAAAAA...AAA
DNA
Primary transcript(hnRNA) MeG cap Poly-A tail
Transcription
They function in the stability of the message and in helping ribosomes bind to the RNA’s 5’ end.
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 8Why do introns exist?
AAAAAA...AAA
DNA
Primary transcript(hnRNA) MeG cap Poly-A tail
Transcription
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.
However protein-nucleic acid complexes in the nucleus of eukaryotic cells recognize
certain sites ( ) in the message.
Study Question 8Why do introns exist?
AAAAAA...AAA
AAAAAA...AAA
Splicing
Primary transcript(hnRNA)
Processedtranscript(mRNA)
MeG cap Poly-A tail
Intron
Exon
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 8Why do introns exist?
AAAAAA...AAA
AAAAAA...AAA
Splicing
Primary transcript(hnRNA)
Processedtranscript(mRNA)
MeG cap Poly-A tail
Intron
Exon
It is the mature, processed transcript that enters the cytoplasm and is translated by ribosomes.
Study Question 8Why do introns exist?
AAAAAA...AAA
AAAAAA...AAA
Splicing
Primary transcript(hnRNA)
Processedtranscript(mRNA)
MeG cap Poly-A tail
Intron
Exon
Where are introns when translation takes place?
…what role [does] an
intron plays in translation?
Study Question 8Why do introns exist?
AAAAAA...AAA
AAAAAA...AAA
Splicing
Primary transcript(hnRNA)
Processedtranscript(mRNA)
MeG cap Poly-A tail
Intron
Exon
You could answer this question the same way you discovered
what is the beginning of a gene.
What would you need to do this?
…could you explain… how a cell's apparatus
distinguishes exon from intron?
Study Question 8Why 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 8Why 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 8Why do introns exist?
Small differences amongst vertebrate
DNA sequences
Large differences in morphology
http://uncyclopedia.wikia.com/wiki/User:Skinfan13/Upsilon_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 8Why do introns exist?
Hormone-responsive protein kinase
hormoneresponsiveness
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.
The first part of the gene encodes the part of the protein that
recognizes the hormone, and the rest encodes the enzyme.
Study Question 8Why do introns exist?
Hormone-responsive protein kinase
hormoneresponsiveness
DNA bindingprotein kinase
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 8Why do introns exist?
hormoneresponsiveness
DNA bindingprotein kinase
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 8Why do introns exist?
hormoneresponsiveness
DNA bindingprotein kinase
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.
Hormone-responsive DNA-binding protein
Study Question 8Why do introns exist?
hormoneresponsiveness
DNA bindingprotein kinase
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.
Hormone-responsive DNA-binding protein
Welcome toIntroduction to Bioinformatics
Wednesday, 25 JanuaryIntroduction to Molecular Biology
Part 2: DNA to protein
• Coming attractions!• Significance• Palindromes (SQ4)• Why introns? (SQ8)• Types of mutation (SQ12)
Study Question 12Single mutation from AGA
If this question is confusing, take it apart bit by bit.
Study Question 12Single mutation from AGA
…the AGA codon… That, at least, might be clear.
Write it down!
AGA arginine
Study Question 12Single mutation from AGA
…a single basepair mutation… What could that mean?
AGA arginine
Study Question 12Single mutation from AGA
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?
AGA arginine
Study Question 12Single mutation from AGA
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’?
AGA arginineTCT
Study Question 12Single mutation from AGA
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?
AGA arginineTCT
5’-3’-
-3’-5’
Study Question 12Single mutation from AGA
That’s one basepair.
What are some possible changes?
AGA arginineTCT
5’-3’-
-3’-5’
Study Question 12Single mutation from AGA
OK, that’s one possible change.
How many total possible changes are there?
Note I said “possible”. A G/A basepair is not possible.
AGA arginineTCT
5’-3’-
-3’-5’
GGA arginineCCT
5’-3’-
-3’-5’
Study Question 12Single mutation from AGA
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’.
AGA arginine
Study Question 12Single mutation from AGA
Moving on, what could “encoding arginine” mean?
I’ll pause so you could look up what arginine is. (Google is your friend)
AGA arginine
Study Question 12Single mutation from AGA
…an amino acid.
Codons encode amino acids.
AGA arginine
Study Question 12Single mutation from AGA
So putting it all together….
…what does the first part of the question mean?
AGA arginine
Study Question 12Single mutation from AGA
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?
AGA arginine
Study Question 12Single mutation from AGA
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
AGA arginine
Study Question 12Single mutation from AGA
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.
Proteins, Figure 2 Proteins, Figure 1
Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub
Study Question 12Single mutation from AGA
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?
Proteins, Figure 2 Proteins, Figure 1
Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub
Study Question 12Single mutation from AGA
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?
Proteins, Figure 2 Proteins, Figure 1
Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub
Study Question 12Single mutation from AGA
Proteins, Figure 2 Proteins, Figure 1
Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub
All the negatively charged R groups have free
carboxylate moieties ( ), with negative charges.
Positively-charged R groups?
-C-O-
O
Study Question 12Single mutation from AGA
Proteins, Figure 2 Proteins, Figure 1
Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub
All positively charged nitrogen atoms in some form.
Finally, the hydrophilic, uncharged R groups?
Study Question 12Single mutation from AGA
Proteins, Figure 2 Proteins, Figure 1
Derived from Elseth & Baumgardner, Principles of Modern Genetics (1995), West Pub
…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.
Study Question 12Single mutation from AGA
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.
AGA arginineGGA ???
Study Question 12Single 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 12Single 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 12Single 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?
• If "conservative" is "close enough", how close is that?
Study Question 12Single mutation from AGA(Frequently asked questions)
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.
• If "conservative" is "close enough", how close is that?
Study Question 12Single mutation from AGA(Frequently asked questions)
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.
• Do we have to learn the 20 amino acids?
• If "conservative" is "close enough", how close is that?
Study Question 12Single mutation from AGA(Frequently asked questions)
Well now, funny you should ask!
• Do we have to learn the 20 amino acids?
• Will we be able to decipher the genetic code of an alien being?
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 Genetic Code
Terrestrial ribosomes
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.
CCCCCCCCCCCC
Alien Genetic Code
Alien ribosomes
? ? ?
`
Alien Genetic Code (Coming Attractions!)
But using alien cell extracts... who knows?
You can know.