Download frame-shift mutation

In This Lesson:
Mutations,
Introns, Exons
(Lesson 3 of 3)
Today is Tuesday,
December 1st, 2015
Pre-Class:
Where does transcription take place?
Where does translation take place?
What is the name for a group of three mRNA bases?
What about three tRNA bases?
You need your Universal Genetic Code tables.
Today’s Agenda
• Mutations!
• Whippet
Normal Whippet
with single
base genetic
mutation
http://media.canada.com/idl/vitc/20070625/2192-640.jpg
http://static.gotpetsonline.com/pictures-gallery/dog-pictures-breeders-puppies-rescue/whippet-pictures-breeders-puppiesrescue/pictures/whippet-0027.jpg
Today’s Agenda
• First, how does all this stuff start up?
That’s our focus for today.
– BTW, we’re talking both prokaryotes and eukaryotes!
• Then, we’re going to add one more little
detail to transcription: exons and introns.
• Where is this in my book?
– P. 194 and following…
By the end of this lesson…
• You should be able to evaluate the effects
of errors in the replication or transcription
processes.
• You should be able to identify sections of
the DNA molecule based on whether or not
they are transcribed.
Chromosome Mutations
• Most of the mutations we’re going to talk
about today have to do with specific bits of
DNA.
– (DNA mutations)
• There are several really bad ones, though, that
have to do with entire chromosomes or
chromosome pieces “going wrong.”
– (Chromosome mutations)
Chromosome Mutations
• Deletion
– A chunk of the
chromosome is lost.
• Duplication
– A part of the
chromosome is copied.
• Inversion
– A part of the
chromosome is flipped.
• Others on next slides…
http://depts.washington.edu/chdd/outlook/images/LgChromosomalChanges.png
Nondisjunction
• Nondisjunction basically means the chromosomes
didn’t come apart properly in meiosis.
– Nondisjunction is the cause of Down Syndrome and related
aneuploid defects.
• It occurs when, during metaphase and anaphase, the
spindles attach to the wrong set of chromosomes, so
they’re not split evenly.
• Animation:
– http://www.biostudio.com/d_%20Meiotic%20Nondisjuncti
on%20Meiosis%20I.htm
Nondisjunction (Meiosis I)
Start meiosis with one
diploid cell that has 46
chromosomes.
46
End with sperm or egg
cells that have the wrong
number of chromosomes.
NONDISJUNCTION
24
24
22
24
22
22
Nondisjunction (Meiosis II)
Start meiosis with one
diploid cell that has 46
chromosomes.
46
End with sperm or egg
cells that have the wrong
number of chromosomes.
23
23
NONDISJUNCTION
23
23
24
22
Side Note: Maternal Age
• Interestingly, risk of Down Syndrome (and other
trisomies) increases with maternal age.
• Mom’s age | risk of Down | risk of trisomy:
–
–
–
–
–
–
Age 20 |
Age 25 |
Age 30 |
Age 35 |
Age 40 |
Age 45 |
1 in 1667
1 in 1250
1 in 952
1 in 385
1 in 106
1 in 30
| 1 in 526
| 1 in 476
| 1 in 384
| 1 in 192
| 1 in 66
| 1 in 21
http://downsyndrome.about.com/od/diagnosingdownsyndrome/a/Matagechart.htm
Translocation
• During crossing over, a part of a
chromosome winds up on another, nonhomologous chromosome.
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Mutations.html
Translocation Analogy
• Imagine you’ve got two copies of the same
book (let’s say, the dictionary).
• If you tore out the last 50 pages of each and
put them in the other book, you’d still have a
complete dictionary.
– That’s normal crossing-over.
• However, if you took the dictionary and the
autobiography of Mickey Mouse, you’d end up
with two very jumbled endings.
– That’s translocation.
Mutation Introduction
• Video: Mutations
DNA and RNA Mutations
DNA
RNA
Protein
Trait
• Today, for simplicity’s sake, we will be
talking about RNA mutations.
– RNA mutations lead to protein changes which
lead to trait changes.
• Of course, there are also DNA mutations.
– DNA mutations lead to RNA mutations…which
lead to protein changes and trait changes too.
Mutations
• Kinds of mutations:
– Point Mutations (occur at only one base):
• Insertion/Deletion (InDel Mutations)
• Substitution
– Transition – purine to purine or pyrimidine to pyrimidine
– Transversion – purine to pyrimidine or pyrimidine to purine
• Point mutations are sometimes called Single
Nucleotide Polymorphisms (SNPs).
Mutations
• Results of mutations:
–
–
–
–
Frame-shift mutations
Missense mutations
Nonsense mutations
Neutral/silent mutations (no effect)
AUG UUU GAG UGA UCC
•
•
•
•
•
Methionine
Phenylalanine
Glutamate
[Stop]
[Serine]
AUG UUU GAG UGA UCC
• Mutation 1: What if I add a C here?
– This is an insertion mutation.
• AUG UUU CGA GUG AUC C
• What happens?
–
–
–
–
–
Methionine
Phenylalanine
Arginine
Valine
Isoleucine
• No stop codon!
AUG UUU GAG UGA UCC
• Mutation 1 is what is called a frame-shift
mutation because all the following codons are
“shifted over.”
• In other words, frame-shift mutations are bad
news because they throw off the whole
resulting protein.
• Mutation 1 is also a missense mutation
because it changed an amino acid (or stop)
codon to a different amino acid.
Frame-Shift Analogy
• Imagine you are bubbling-in answers on a
standardized test and decide you want to
skip a question and return to it later.
• However, on your answer sheet, you don’t
skip a line. What happens?
– All your following answers are thrown off by
one, just like a frame-shift.
Put it another way…
• Taking code like AUGCCCCAUUUU and making it
AUG|CCC|CAU|UUU is adding a reading frame.
– Sort of like the spaces in the sentence:
“THE RED DOG ATE THE BIG BUG.”
• Screw up the reading frame and you have an
issue.
– Sort of like trying to read:
“TH ERE DDO GAT ETH EBI GBU G.”
• A single spacing issue has a wide-ranging effect.
AUG UUU GAG UGA UCC
• Mutation 2: What if I add the AAA codon here?
– (not a frame-shift)
• AUG UUU AAA GAG UGA UCC
• What happens?
–
–
–
–
–
Methionine
Phenylalanine
Lysine
Glutamate
[Stop]
• There’s an extra amino acid, but not a frame-shift
mutation. Bad, but not that bad.
AUG UUU GAG UGA UCC
• Mutation 3: What if I add a GA here?
– This is a frame-shift mutation.
• AUG UGA UUG AGU GAU CC
• What happens?
– Methionine
– [Stop]
• The early stop codon prevents the full
protein from forming.
AUG UUU GAG UGA UCC
• Mutation 3 is also called a nonsense
mutation because it took a normal protein
and terminated it early.
• The protein “makes no sense,” thus, a
nonsense mutation.
AUG UUU GAG UGA UCC
• Mutation 4: What if I delete this A?
– This is a deletion mutation.
• AUG UUU GAG UGU CC
• What happens?
–
–
–
–
Methionine
Phenylalanine
Glutamate
Cysteine
• No stop codon expressed - protein keeps going!
AUG UUU GAG UGA UCC
• Mutation 5: What if I change this A to a G?
– This is a substitution mutation.
• AUG UUU GAG UGG UCC
–
–
–
–
–
Methionine
Phenylalanine
Glutamate
Tryptophan
Serine
• No stop codon expressed - protein keeps going!
AUG UUU GAG UGA UCC
• Mutation 6: What if I change this U to a C?
– This is a substitution mutation.
• ACG UUU GAG UGA UCC
• No start codon expressed - protein never formed!
AUG UUU GAG UGA UCC
• Mutation 7: What if I change this A to a U?
– This is a substitution mutation.
• AUG UUU GUG UGA UCC
–
–
–
–
–
Methionine
Phenylalanine
Valine
[Stop]
[Serine]
• Glutamate is changed to Valine.
• Not a frame-shift mutation (is a missense).
– Unfortunately, this is all it takes to get sickle-cell anemia.
Sickle-Cell Anemia
• Protein in red-blood cells is
deformed to the point that
they’re not happy round
red-blood cells.
• Limited oxygen-carrying
capacity and painful blood
flow.
– (draw a picture)
http://adultstemcellawareness.files.wordpress.com/2007/10/sickle-cell.jpg
Sickle-Cell Anemia
http://www.nhlbi.nih.gov/health/health-topics/topics/sca
Sickle-Cell Anemia
• Video
AUG UUU GAG UGA UCC
• Mutation 8: What if I change this U to a C?
– This is a substitution mutation.
• AUG UUC GAG UGA UCC
–
–
–
–
–
Methionine
Phenylalanine
Glutamate
[Stop]
[Serine]
• No change - this is a neutral mutation!
Neutral Mutations
• Mutation 8 shows that not all mutations
can cause problems.
• This is what scientists think is part of the
reason for there being many more codons
than there are amino acids.
• Neutral mutations are often called silent
mutations.
Challenge
• AUG UUU CAU UGA UCC
• What happens if I change this G to an A?
Transcriptlate Lab
• Now it’s time to try #5 on the lab.
• Example DNA strand (line 1) is:
– AACTGGACT
That last one’s a stop codon.
• Suppose we delete the fourth base – what
Old Codon
New Codon
happens?
DNA Strand
TGG
GGA
RNA Strand
ACC
CCU
Amino Acid
Threonine
Proline
• There is a frame-shift mutation.
• Threonine is changed to Proline – a missense
mutation.
• Our stop codon has been deleted.
So after all of this…
• How is it a person can naturally have two
different color eyes?
• Mutations!
• Now for my question to you:
– Is it a mutation in the mRNA or the DNA?
Why?
DNA vs. RNA
• To answer this question, use an analogy:
• Imagine I’m baking a cake, but I
accidentally put in 4 sticks of butter instead
of 2.
– My cake will taste like poo.
• If I bake it again, however, I probably won’t
make the same mistake twice.
– My cake is awesometastic.
DNA vs. RNA
• However, what if it’s not really my
mistake? What if the recipe has a typo in
it?
– I will continue making the same mistake each
time I follow the recipe.
– All my cakes will taste like poo.
DNA vs. RNA
• In the case of the cell, if a mistake is made
in the RNA, it’s probably not a big problem.
– One bad protein in one cell won’t kill you.
• But what if it’s a mistake in the DNA?
– All proteins will be malformed.
– This is especially bad if the DNA experiences a
mutation early in pregnancy.
Therefore…
• People that have two different eye colors,
or some other kind of lasting mutation,
likely have a mutation in their DNA, not
their RNA.
Now for an activity…
• Lightly stick your piece of masking tape to
the desk horizontally.
• Write exactly the following on it, making
sure to leave some space between all the
letters:
APproPRIAteLY JOinED
APproPRIAteLY JOinED
• Now, carefully tear your letters apart so
you have separate sequences of lower case
and capital letters.
– In other words, whenever the case changes,
tear between those two letters.
• Junk the capitals…what did you spell?
Uh…huh.
• Okay, so what’s the point?
• It turns out, not all of an mRNA molecule is made
into proteins.
– Only some sections are; the rest are “junk.”
• So why make the junk in the first place?
• Well, suppose some damage to the mRNA occurs.
– If all of the mRNA is important, our protein will be
deformed.
– BUT! If some of the mRNA is junk and damage occurs,
the damage may not affect the important parts of the
mRNA.
Exons and Introns
http://upload.wikimedia.org/wikipedia/commons/1/12/DNA_exons_introns.gif
Exons and Introns
• Exons (lower-case letters) are the parts of
mRNA that are expressed (not cut out).
• Introns (capital letters) are the parts of
mRNA that interrupt (are cut out).
– This happens in the nucleus.
– Cut by structures called spliceosomes.
The Big Summary of
Transcription & Translation
•
•
•
•
DNA in the _______.
nucleus
We start with _______
transcribed into _______.
mRNA
DNA is _________
Introns are removed, while _______
exons are kept.
_______
mRNA leaves the nucleus and goes to the
ribosome in the cytoplasm.
_______
amino acids
• mRNA is translated into a chain of __________,
polypeptide
which makes up a _________.
• Ta-da!
Don’t Forget the Enzymes!
• Which enzyme unwinds the DNA helix and breaks
the hydrogen bonds holding together the two
sugar-phosphate backbones during replication?
– DNA Helicase
• Which enzyme places new RNA nucleotides on the
growing mRNA strand during transcription?
– RNA Polymerase (also unwinds DNA helix)
• Which enzyme places new DNA nucleotides on the
growing DNA strand during replication?
– DNA Polymerase
Don’t Forget the Enzymes!
• Which enzyme seals gaps between Okazaki
fragments?
– Ligase.
• Which enzyme works before DNA
Polymerase and lays down a small
foundation of RNA bases before DNA
Polymerase starts laying down DNA bases?
– Primase.
Turning It On and Off
• First the prokaryote example:
• Meet
Barry the Bacterium. He likes
Mmmmm!
lactose,
thelactose!
sugar found in milk. He
I love
me some
doesn’t get it all the time, though,
and he needs a special group of
enzymes to digest it.
Barry’s Choice
• Help a bacterium out. Barry can do one of
two things:
1. Barry can make those lactose-related
enzymes all the time, and then use them
every once in a while when he gets some
lactose.
2. Barry can wait till he gets lactose, then make
some of those enzymes.
• Which makes more sense biologically?
Barry’s Choice
• Another way to think about it:
– If I go to the grocery store, would it be
worthwhile for me to buy a year’s worth of
groceries all at once?
• Imagine one year’s worth of produce, bread, ice
cream, et cetera…
Barry Made the Right Choice
If I were
a real bacterium,
• Transcription
and translation cost
I wouldn’t have a face.
energy, so it’s best to do them
only when necessary.
• Prokaryotes use something called
a repressor to block the genes for
the lactose enzymes, which we
call the lac operon.
– An operon is like a group of genes.
Let’s look at an animation…
• PhET – Gene Machine: The Lac Operon
On and Off
• The repressor binds to the DNA in the
nucleus and just sits there, blocking RNA
polymerase.
– No Transcription!
• Eukaryotes have the opposite. Instead of a
repressor needing to get out of the way, an
activator and transcription factors need to
bind to get things started.
Repressors and Activators
Activator binding to mRNA
The more
realistic
version
of transcription
Repressor
leaving
mRNA
http://www.nature.com/nrm/journal/v5/n5/images/nrm1369-i1.gif
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=cooper&part=A964&rendertype=figure&id=A974
The Big Picture (Eukaryotes)
• Inside the nucleus:
– An activator and transcription factor bind to
DNA.
– DNA is transcribed to mRNA by the enzyme
RNA polymerase.
– Introns are removed by spliceosomes.
– mRNA leaves the nucleus.
The Big Picture (Eukaryotes)
• Outside the nucleus:
– The two rRNA subunits of the ribosome come
together on mRNA.
– mRNA is translated in the A and P sites.
– tRNA helps string together amino acids to
make a protein.
– A stop codon releases everything.
Closure
• Transcriptlate Lab
– Finish it!
• Remember, if there’s a frame-shift, be sure
to check “downstream” of the mutation.
– Frame-shift errors often lead to problems with
the stop codon.
• Whether it gets deleted or shows up early.
Exit Ticket
• Define the following in your own words:
– Exon
– Intron
• How can you remember these?
– Saying, “I just can!” isn’t good enough. Hint: Think
about why we call them exons and introns.