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Pile Management Card
Molecular Bio

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What if you end up with a gene duplication?
*The boring consequences would be that you might wind up making a lot more of that gene’s protein.
*One gene can conserve original function and the new gene can take on a new role.
Reconciling micro- and macroevolution
*A mutational change in a single nucleotide in a gene can change how well a protein does its job, potentially producing a gradualist, microevolutionary shift.

*A change of a single nucleotide in an exon of overlapping genes can be quite deleterious, can be highly selected against, providing a mechanism for stasis.

*A change of a single nucleotide in a promoter, or in a gene coding for a splicing enzyme, a transcription factor, or an enzyme that mediates transposon movement, can produce a completely novel protein, or changes in entire networks of proteins.

*Transpositions of exons and of promoters can produce entirely new proteins and new if-then clauses.
What is an evolutionary bottleneck?
*Evolutionary bottle necks are responsible for periods of rapid change.
*Suppose a meteor hits earth. Environment wet -> dry. There is a mutation where only 2 peeps can retain water effectively. Those 2 peeps will survive and their genes will become highly prevalent in the next generation.
How does evolutionary change ever occur?
evolutionary bottleneck
How does stasis happen?
Most macroevolutionary changes are likely to be majorly disadvantageous when it comes to passing on copies of genes. And thus they will be selected against, producing stasis.
What if, thanks to a transposable event, if a transposition occurs with a promoter, if it is moved from one part of the genome to another, winds up being upstream of a different gene?
You've created a new if then clause.
What happens if there is a mutation in an enzyme that clips out and reinserts a transposon?
Just like with mutations in splicing enzymes – you can potentially produce a completely novel gene, moving some exon from one gene and plunking it down in the middle of another.
Mutation in TF
TF may work on a completely new set of genes.
overlapping genes
, the string of amino acids coded for by Exon A might wind up in half a dozen different proteins (the one coded for by Exons A and B; the one coded for by Exons A, C and D…..). Thus, a mutation in Exon A could wind up changing the function of an array of proteins.
What are epigenetic changes?
Cases where gene expression is changed for a lifetime
What is chromatin?
An additional layer of regulation of gene expression (i.e., when a gene is activated).
*In order for a transcription factor to get to a particular promoter, the chromatin ensheathing around there has to loosen, open up a bit, to allow the transcription factor in.
What activates transcription factors?
The environment, and this can mean several things.

*intra-cellular
*inter-cellular
*outside of organism
How does a gene “decide” when to have some RNA photocopies made of itself and make some of its cognate protein constructed?
The gene doesn’t decide; the gene hasn’t a clue!

*Instead, a regulatory type of protein called a transcription factor binds to the promoter stretch of DNA, and that activates the nearby (“downstream”) gene.

*Or there are non-transcribed stretches of DNA which, when bound to by some different type of transcription factor, deactivate the downstream gene – a repressor element in the DNA.
95% of DNA does not code for anything
The stuff that codes for stuff = exons.

What is everything else?
-introns
-promoters
-repressors
Transposons (possible mechanisms for punctuated equilibrium)
*There exist enzymes that can clip out stretches of DNA and insert them in other places in the genome.

*Example: Plants can't move. It makes sense that they try to come up with different things that may work to their advantage by reshuffling their genome.
Mutations in promoters or repressors (possible mechanisms for punctuated equilibrium)
*You can have a mutation in a promoter sequence, such that the boring old transcription factor that turns it on no longer does, potentially silencing the gene.

*Or, maybe the new promoter sequence is now recognized and activated by a completely different transcription factor

*If we have a mutation in a repressor, a TF may not be able to recognize the repressor, thus it won't bind and we will not silence the gene that we need to.

*Or, maybe the new repressor will be recognized by a new TF that binds to it.
Alternative splicing (a possible mechanism for punctuated equilibrium)

*How do you produce a single intact protein out of a gene that’s made up of a zillion separate exons?
*Enzymes splice out the intronic part, paste together the exons into a single RNA message that now codes for a protein.

*Since we can specify multiple proteins out of a single stretch of DNA, with the assistance of different splicing enzymes, a process called alternative splicing...
-If we have a mutation in the enzyme (a protein) that usually splices at spot X, it will not splice there anymore. In fact, it will probably splice somewhere else, forming a different collection of exons that will give rise to a different protein.
What are ways in which macroevolution can occur (punctuated equilibrium)?
*Alternative splicing

*Mutations in promoters or repressors

*Transposons
What are some criticisms to punctuated equilibrium?
*If paleotonologists are not seeing gradual, incremental change in some fossil pedigree, it’s because there’s a whole lot of intermediate fossil forms that haven’t yet been discovered – the fossil record is incomplete

*the critics point out, lightening fast, blink-of-an-eye change, to a paleontologist, is tens of thousands of years. A lot of microevolution, a lot of sociobiology can go on in a dozen millennia -- paleontologists think in different time scales than lots of behavioral scientists.

*None of the good, interesting stuff is detectable by paleontologists (soft tissue stuff).

*What are the molecular mechanisms to explain how rapid, major macroevolutionary change might occur?
What about punctuated equilibrium devastates the sociobiologists?
if there is a period of evolutionary stasis, where no major changes are occurring, then sociobiology – with its premise of every little bit of genetically based difference mattering in this competitive world of maximizing your reproductive success – is irrelevant
What is punctuated equilibrium?
Periods of long stasis (no change) followed by abrupt periods of rapid change (saltatory).
MOLECULAR BIOLOGISTS subscribe to microevolution or macroevolution?
MACROEVOLUTION = punctuated equilibrium.
SOCIOBIOLOGISTS subscribe to microevolution or macroevolution?
MICROEVOLUTION!!! = Gradualism

*Incrementally changing the genetic makeup of a species leading to differences in behavior.
How does microevolutionary change apply to the evolution of behavior?
*First off, microevolutionary change is when a mutation gives rise to a protein that has a different function that the non-mutated version.

*There are two examples.
-PKU: The body is capable of detoxifying itself when it ingest something dangerous. A particular protein is responsible for detoxifying. If this protein is mutated, we will not be able to detoxify. The brain will experience a build up of toxic substance, causing neuronal damage. Obviously, this will affect someone's behavior.

-Testosterone: say the receptor for testosterone experiences a mutation that allows it to bind to testosterone molecules longer. This will lead the person to become more aggressive.
What is random drift?
It means that the differences in amino acids between populations can be explained by the expected rate of change, 1/3
What are codons?
Base pair triplets that code for a particular amino acid.
What is positive selection?
*Amino acid changes are occurring at a greater rate than chance would expect (1/3 rate).

*It means that changes in the resulting protein were adaptive, and that's why the changes are continuing to be seen.
What is negative/stabilizing selection?
*It means that amino acid changes are occurring at a slower rate than chance would expect (1/3 rate).

*The implication is that the protein is so important in its current form and that any change will have detrimental effects.
Insertion mutations
*What is it?
-You insert a nucleotide.

*Will it cause a change in protein?
-Yes, frame shifts have major consequences.
Deletion mutation
*What is it?
-During replication, instead of changing a nucleotide from one thing to another, a nucleotide is completely deleted.

*Will it cause a change in protein?
-Yes. Because a nucleotide is deleted, this shifts the entire frame, and so everything downstream is affected (you can even delete multiple nucleotides at a time, deleting entire genes).
Neutral mutations
*What is it?
-When the same amino acid the non-mutated gene would have coded for is still produced from a mutated gene.

*Will it cause a change in protein?
-Nope.
Point mutations
*What is it?
-a single base pair is mutated (e.g. we go from A -> T)

*Will it cause a change in protein?
-Maybe.
-No: due to the redundancy of the genetic code, the change may not matter because the sequence may code for the amino sequence that the nonmutated gene would have coded for (this is called NEUTRAL MUTATION).
-Yes: the same amino acid is not coded for.
What are the different types of mutations?
*Point mutations
*Neutral mutation
*Deletion mutation
*Insertion mutation.
How do individuals end up with different versions of proteins?
Mutations.
What does it mean to say that there are different versions of heritable traits?
The importance is that it means that slightly different version of the gene will give rise to slightly different proteins.
What does, "some traits are heritable" mean?
It means that my genes (DNA sequences), are inherited from my parents
What are the basic tenets of evolution?
*some traits are heritable
*different versions of heritable traits
*the more adaptive version means the better reproductive success
Where does the central dogma fail (Watson Crick)?
We can also go from RNA -> DNA with reverse transcriptase.
Why is this wrong, "one type of gene specifies one type of protein"
Different trios of nucleotides can code for the same amino acid.
So what determines the sequence of amino acids?
Genes! When we go from DNA -> RNA -> protein, the sequence of nucleotides in the DNA affects everything else downstream.
Why is the amino acid sequence important?
Because it determines the shape of the protein. The shape of the protein determines the function of the protein.
What makes up proteins?
Strings of amino acids.
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