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.

In This Lesson:Mutations,

Introns, Exons(Lesson 3 of 3)

Today’s Agenda

• Mutations!

http://static.gotpetsonline.com/pictures-gallery/dog-pictures-breeders-puppies-rescue/whippet-pictures-breeders-puppies-rescue/pictures/whippet-0027.jpg

http://media.canada.com/idl/vitc/20070625/2192-640.jpg

• Normal Whippet• Whippet with single base genetic mutation

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%20Nondisjunct

ion%20Meiosis%20I.htm

Nondisjunction (Meiosis I)

46

24 22

Start meiosis with one diploid cell that has 46

chromosomes.

24 24 22 22

End with sperm or egg cells that have the wrong

number of chromosomes.

NONDISJUNCTION

Nondisjunction (Meiosis II)

46

23 23

Start meiosis with one diploid cell that has 46

chromosomes.

23 23 24 22

End with sperm or egg cells that have the wrong

number of chromosomes.

NONDISJUNCTION

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 | 1 in 1667 | 1 in 526– Age 25 | 1 in 1250 | 1 in 476– Age 30 | 1 in 952 | 1 in 384– Age 35 | 1 in 385 | 1 in 192– Age 40 | 1 in 106 | 1 in 66– Age 45 | 1 in 30 | 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, non-homologous 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

• 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.

DNA TraitProteinRNA

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• Suppose we delete the fourth base – what

happens?

• There is a frame-shift mutation.• Threonine is changed to Proline – a missense

mutation.• Our stop codon has been deleted.

Old Codon New Codon

DNA Strand TGG GGA

RNA Strand ACC CCU

Amino Acid Threonine Proline

That last one’s a stop codon.

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 ofTranscription & Translation

• We start with _______ in the _______.• DNA is _________ into _______.• _______ are removed, while _______ are kept.• mRNA leaves the nucleus and goes to the

_______ in the cytoplasm.• mRNA is translated into a chain of __________,

which makes up a _________.• Ta-da!

DNA nucleus

transcribed mRNAIntrons exons

ribosome

amino acidspolypeptide

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

lactose, the sugar found in milk. He doesn’t get it all the time, though, and he needs a special group of enzymes to digest it.

Mmmmm!I love me some lactose!

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

• Transcription and translation cost 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.

If I were a real bacterium,I wouldn’t have a face.

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

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=cooper&part=A964&rendertype=figure&id=A974

http://www.nature.com/nrm/journal/v5/n5/images/nrm1369-i1.gif

Repressor leaving mRNAThe more realistic version of transcription

Activator binding to mRNA

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.