[Instructor] Hello and welcome to Module 5.
So we will go through
three different lectures in this module.
And the first one we're going to start with
really thinking about how to piece together
some of what we've learned in the first couple of modules
to expanding that to patterns of inheritance
and the actual traits that you see.
So we're gonna start this with lecture called
genotype to phenotype.
And as you remember, a genotype is the sequence
of a particular gene.
So if someone has, say a disease mutation that
it causes a disease, it's the actual mutation,
the sequence of the gene itself, that's the genotype.
The phenotype is the trait.
That's actually what you see in a person.
And that might be the disease.
It might be something else like eye color, hair color,
height, these are all traits,
these are all phenotypes that are affected,
in some cases directly caused by,
and in some cases just affected by
a particular gene sequence or the genotype.
So genotype determines phenotype.
So that we're going to actually take this
and look into it in a little bit more depth
and better understand how can we transition from
what we've learned about gene sequences and gene expression
and transition that to the actual traits that we see.
And take that into the next couple of lectures
where we start to think about patterns of inheritance
that you might record, say in a pedigree
from a family history that a patient might give you.
Let's do a quick review.
DNA sequence is copied into mRNA during transcription.
mRNA sequence is read as codons
or triplets of bases in a specific order.
And this will become really important when we start talking
about different kinds of mutations
and the impact that can have on the protein
that's made from the instructions from this gene.
During translation, each codon encodes for one amino acid
or instructs the ribosome to stop translation.
So you remember that there are 20 different amino acids
and each one of those has a couple of different codons
that can encode for it.
And a codon, as you recall, is just a set
of three bases together, but in a specific order.
So if you remember, there was that codon table
and you can double check that if you'd like
to refresh your memory of what that actually was.
But it's that table and you have basically the first base on
the left hand column,
the second base going horizontally across,
and then the third base going down on the right hand column.
And you can look on the table for any combination
of three bases and see which amino acid it encodes
or if it encodes for a stop signal, for example.
Proteins are made up of a chain of amino acids,
strung together in a specific order
to give the protein its specific shape and function.
Proteins do virtually everything in a cell
so getting the amino acids sequence exactly correct
is really important.
And in some proteins, in some specific parts
of certain proteins, if there are changes in amino acids,
it may not actually affect the protein's function,
but certainly for others there are regions of the protein
where getting the exact amino acid in the exact right order
is absolutely critical and can completely change
or even eliminate the normal function of the protein.
Here are a few important terms and definitions
that we'll talk about in this particular lecture.
So first of all, genotype.
This is the nucleotide sequence of a gene.
So genotype is the sequence of a particular gene.
The phenotype, this is the trait or characteristics
seen in a person.
So an example would be the presence of a disease.
Another example of a phenotype would be eye color or height
or whether or not a person develops type 1 diabetes.
These are all called phenotypes.
So it's basically what you would see
or experience in a person.
The genotype is the DNA sequence for the particular genes
that would affect the phenotype.
And allele, this is an important definition in one
I'd like you to try to pick up on,
because we're going to start using this term a lot.
And it's important that you understand what it means
because otherwise it can get kind of confusing.
But an allele is one of the alternate versions of a gene.
And what I mean by that is,
let's take for example, the eye color gene.
Let's say we actually have a couple of different genes
that affect eye color, but let's make it simple
and just say there's one gene that affects eye color.
So you would have in, say, 10 different people,
you might have three or four different eye colors.
You could have green, brown, blue,
even like a grayish color.
And you know, there are many other colors.
But basically what we're talking about when we're talking
about an allele, if we think about that eye color gene,
let's say, so it's a gene which encodes a protein
which impacts directly the eye color of an individual.
And a person who has brown eyes, they would have an allele
for a brown eye color for that particular eye color gene.
And another person, they might have a blue eye color allele.
So the allele is just basically a different version,
a slight modification in the sequence of a gene,
which impacts the phenotype.
So it would give you a different phenotype or, you know,
slightly different outcome for that particular trait.
So alleles, you can have many different alleles
sort of in the general population for a particular gene,
you know, you might have hundreds
or more different versions,
slight variations on a particular gene.
Each person will only have two alleles
because you have two copies of each gene.
So you might have two alleles that are exactly the same.
Let's go back to the eye color example.
Maybe both of your parents had blue eyes
and let's say they both donated to you the blue eye allele.
So say you'd have blue eyes in that case,
and both of your alleles, both of your copies
of the eye color gene would be for the blue eye color.
You can also have two different alleles.
So two slightly different versions of the same gene.
And then the question becomes, what would your phenotype be
if you have two different alleles?
Well, we'll talk about that in a lot of detail
in the next lecture.
So hold on to those questions.
A SNP or single nucleotide polymorphism is a single base
change in a DNA sequence,
which may or may not be associated with a phenotype.
And what I mean by that is there could be a slight change.
It's basically changing one base to another base.
So an A towards to a T or a C to an A
or something like that.
And that may result in a different amino acid being coded
for if this is occurring within a gene.
And that may or may not impact the proteins function,
which may or may not impact the phenotype for a gene.
Or it may or may not impact the phenotype
for that particular allele.
All right, wild type is what we would call
the most common allele of a gene.
So we would refer to sort of what you might consider
the normal copy,
especially if we're talking about a disease.
Now this isn't really going to be the case
for something like eye color or hair color
or things like that, but more when we're talking about
a disease versus non-disease versus, you know,
sort of a normal functioning copy.
The wild type is going to really be the normal functioning
version of a gene, but it's considered wild type.
And it was given that name by earlier geneticists
who were studying genetics in different species of animals.
And they would go out into the wild
and they would, you know, catch their particular animals
that they're studying.
And many of them it was, you know,
fruit flies that they would catch.
And so they would say the most common
phenotypes or traits that they would see,
they would consider those to be the wild ones.
So what you would see out in the wild.
So that's why it actually has the name wild type.
Wild type really just means the normal version,
the very common version
that's mostly seen in the population
Mutant would be the allele with the change in the sequence
compared to the wild type sequence.
And this mutant most likely is related
to a phenotype change.
And in the case of diseases,
most mutant alleles are actually associated
with a person having a disease
or having a greater susceptibility for a disease.
De novo would be what we would refer to as a new mutation
which occurs spontaneously in an individual.
So it was not inherited from his or her parents.
Monogenic is a disease which is caused by a single gene.
For example, in case of a disease,
a mutation in one gene would be sufficient to cause
an individual to have a disease.
Multifactorial diseases, these are diseases which are caused
by multiple genes and/or environmental influences.
And actually, most diseases would fall into the category
of being multifactorial.
So they're influenced not just by one gene, say,
maybe you have a slight influence from 10, 15,
100 different genes
and also could be influenced by the environment.
And that could mean any combination of, you know,
of things in a person, say for example, their diet,
their level of exercise,
any other comorbidities they may have.
All of these may start to impact
and influence a multifactorial disease.
As opposed to a monogenic disease,
which is really directly caused
by a mutation in a single gene.
We'll talk more about monogenic diseases
in the next lecture as well.
Multifactorial diseases, we'll go into those in more detail
in the next module, so next week.
All right, so I sort of gave you an overview with that,
but let's go back one more time
'cause it is pretty important
to get some of these terms correct.
So as you recall there, you have two copies of each gene,
one from each parent, and the genotype
will be the sequence of the gene.
And so for each of us, if we're talking about a gene,
which say is on an autosome, right?
We each have two copies of all of those twos.
So our genotype, we would have the genotype for
both the maternal and our paternal copies of each gene.
The phenotype is the trait or characteristic
seen in the patient.
And that would be in the case of what we'll be discussing
more sensibly, that would be, say,
having a disease or not having a disease.
And these copies or alleles may have slight differences.
And we talked about this a moment ago
with eye color gene in the population one allele
or sequence variant codes for brown eyes, one for blue,
one for green, but they are all the same genes
when we're talking about different alleles.
These are different alleles of the same gene.
A protein dysfunction related to a disease
results from the patient having at least one
copy of the gene with the disease or disrupted sequence
or the disease allele,
or what could be called the mutant allele.
So I just wanna take one more quick moment
to get the concept of alleles down.
And I apologize if this is really being redundant,
but I'd rather be a little bit redundant here
than to just lose you a little bit
when we start throwing around terms like allele wild type,
you know, when we move on in this material.
So here's an analogy that might be useful.
I hope it's useful to you.
If you think of alleles,
let's take an example of a deck of cards, okay?
So like a regular deck of playing cards.
So there are 52 different cards in a typical playing deck.
So if we're using an analogy here,
you can think of this is basically like saying
there's the card gene, right?
So all of the cards in the deck,
even though there are 52 different cards in the deck,
they're all cards, right?
So let's say they're all different versions
of the card gene.
We can call that the card gene.
And there are 52 different versions of it
that would be like saying there are 52
different possible alleles.
You could have the two of clubs,
you could have the five of spades,
you could have the queen of diamonds,
you could have whatever,
let's say there are 52 different alleles
or slightly different versions of cards,
but they're all cards so that they're all alleles
of the same gene.
It's just that they have slight changes.
So you know, a small percentage of the bases are different
between the different copies and the same,
you know, could be true.
If we go back to that analogy of the cards.
So there are 52 different alleles, let's say
in our population in the card gene.
So for each person you get to have two alleles.
Assuming this gene is on an autosome, right?
Not on an X chromosome,
but on an autosome you get to have two copies.
So it's like taking two cards from the deck
and you get whatever you get from that and those two cards.
And you know, let's say we have more than one deck of cards
that are there,
let's say we have five decks of cards, okay?
So there are 52 different cards in the deck,
but each of them is present, you know,
in five different cards.
So when you pull two cards,
you might pull two different cards,
you might pull a two of clubs and a seven of spades,
or you might pull two two of clubs.
And what we'll talk about in the next lecture would be
how our phenotype can be affected
by the two different alleles that we have.
So let's go back for a second to that analogy again,
I apologize if this isn't coming out as clearly
as it is in my head, but it's basically like saying
alleles are slightly different versions of the same gene,
but they're all the same gene.
So they're all cards in our analogy.
And you can have many different alleles
or slightly different versions of a particular gene
in the population as a whole, right?
But each individual person only possesses two alleles.
And those two alleles might be different from one another
and they might be the same as one another.
Okay, I hope that kind of starting
to make sense a little bit.
So let's take a quick peek at what this might mean
and what are these changes that we're talking about?
So small changes in the sequence are called mutations.
So we would consider that the most common sequence
for a particular gene is called the wild type allele.
And any derivation from that in terms
of the sequence would be considered a mutation.
The mutation may be harmful in the end to the person,
it may be completely neutral,
actually most mutations are neutral
or it actually may be slightly beneficial.
And that would be what drives evolution
and progression of a species and adaptation.
We're not gonna really get into that.
We're gonna really more
so focus on the detrimental side of mutations.
But just keep in mind that actually mutations are not
entirely a bad thing, certainly not for a species
because it can provide genetic diversity,
which can be quite beneficial in that
if we're responding to changes in our environment,
those individuals who have an ability to say survive
specific set of conditions could survive
and our species could propagate.
Anyway, we're not gonna really talk
about beneficial mutations,
we're really going to focus on those mutations
which are detrimental.
So mutation is just a slight change.
And let's see, in this particular example,
it would be like taking this sequence here,
let's say we're just showing the single strand
of a genes sequence, okay, that's just one strand
and let's say it was actually mutated.
So that's the wild type say on the top
and on the bottom, this strand here.
So changing that adenine base to a guanine,
this would be a mutant version.
So these could be two different alleles
if they have different phenotypes.
And this one mutation can result in big changes
to the protein function, which can cause disease.
Or again, it may actually have no impact
or it might just have a slight impact.
So let's just take a couple of examples here.
So sickle cell disease,
a mutation in the hemoglobin beta gene results in a change
in the hemoglobin protein,
which affects its shape and function,
the shape and function of hemoglobin.
Mutated hemoglobin forms along in flexible chains
in red blood cells, making them stiff and angular
and likely to become stuck in small capillaries
reducing oxygen delivery to organs.
So as you can see up here, the normal shape of hemoglobin
is basically, you know, a nice sort of balled up shape
and it needs to be that shape
so it can properly bind to oxygen
and can keep keep the red blood cells in the normal shape
that our body has adapted to,
and they can flow freely through capillaries
and deliver oxygen throughout the body.
If however, there is a mutation, it's just actually
a single base change in the hemoglobin beta gene,
that can result in a change in the protein structure
for hemoglobin beta, which can cause it to form
these long and flexible chains,
which can affect the shapes of the cell.
And these hemoglobin proteins
no longer bind oxygen as well either.
So you have the combined effect of the blood cells
getting stuck in capillaries
and not being able to deliver oxygen.
But also when they do get there,
the oxygen is actually not bound as well.
So that's like an example of a change in a protein
affecting an outcome for an individual.
So in this particular case we could be looking at least
two different alleles here, the normal or wild type allele
which would encode the normal functioning hemoglobin here,
and also an allele that has a single base mutation
which would result in the hemoglobin being disrupted
and give the phenotype of sickle cell disease.
All right, let's look at one more example, cystic fibrosis.
So mutations in the CFTR gene affect the CFTR proteins'
ability to move chloride ions in and out of the cell,
resulting in sticky mucus
building up on the outside of the cell.
And in the lungs this mucus buildup can lead to infections,
and in the pancreas, the mucus can block digestive enzymes
from being secreted leading to significant health problems.
So here what we're looking at is on the left hand side,
a drawing of a normal functioning CFTR channel,
which is the protein.
The protein's function is to act as basically like a channel
through which ions can flow in and out of the cell,
but you know, through the cell membrane.
So that's the normal function,
it allows chloride ions in and out as the cell needs it,
and you don't get this buildup of mucus.
If however, there is a mutation in the sequence
for the CFTR gene.
So that would be a mutant allele.
If a person has mutant allele for this,
then the CFTR protein that's encoded would not
function properly because it would not be built properly
because the cell would be told to, basically,
form the CFTR protein
with some changes in the amino acids than what it should be.
Then the protein itself doesn't function properly
and the chloride ions get stuck
and it results in the buildup of mucus.
All right, let's talk about mutations.
So this is a change in A DNA sequence.
New mutations occur randomly from uncorrected
errors in DNA replication.
You remember that, we talked about that.
I believe that was in Module 3,
and from DNA damage by mutagens.
So we'll talk more about mutagens
when we go into the cancer module.
But mutagens are basically like, you can kind of think
of them as like some toxins or chemicals or, you know,
UV radiation from sunlight.
Those types of things can be considered mutagens
and they basically are essentially chemical structures
that enter the cell and will damage DNA and cause mutations.
Mutations could have been inherited from a parent
or could also have occurred spontaneously in an individual.
And these spontaneous mutations,
which result in disease are called de novo mutations.
Three basic types of changes can happen.
And these are the three basic types of mutations.
So point mutation or a change in one base to another base.
And this is sometimes called a SNP,
you remember that from the definitions page,
a single nucleotide polymorphism.
You can probably see why we call it SNPs.
It's a little easier to say that than
single nucleotide polymorphism.
It's kind of a mouthful.
So a point mutation is just a single change,
nothing added, nothing removed.
It's just basically, in this case what we're looking at here
instead of the cytosine in the third position
of the short sequence we're looking at, it's now an adenine.
So it's a C to an A, point mutation,
or change in the sequence.
An insertion would be inserting a new base or bases.
And here we're looking at between the two cytosines,
the third in the fourth, we add a thymine.
So it's now one base longer.
And you could have an insertion of one base of, you know,
any number of bases, 2, 3, 5, 10, 20, however many.
A deletion would be deleting an existing base or bases.
So here we're looking at the TGCC sequences.
Now we're losing one of those cytosines, so it now is TGC.
So one of the cytosines was lost, that's a deletion.
So some possible effects of single nucleotide polymorphisms
on the encoded protein or those point mutations.
The end result, so what can it possibly due to the protein
that could be encoded from this gene?
The mutations could be silent,
which means that while the sequence has changed,
there is no change in the protein encoded.
So this would be, for example,
like a CGG being changed to a CGT.
But both of these actually encode for alanine,
the amino acid alanine.
Go look at your amino acid chart if that's helpful to you.
So the protein is the same either way.
So there's no effect on phenotype,
so this is a silent mutation.
And we actually have quite a few of these
because there's no selection against those.
So individuals will survive.
There'll be no effect whatsoever if this particular kind
of silent mutation occurs because the codon
still encodes for the same amino acid
'cause if you remember, there are only 20 amino acids,
but there's 64 different possible DNA triplets or codons.
You remember that, that occurs in translation
where the ribosome is reading each of the triplets,
each of the codons and each of those triplets,
it's telling a specific amino acid to add.
Well, there's what's called redundancy,
which basically means that, as we talked about before,
since they're only 20 amino acids
and there's 64 different possible codons,
that each amino acid actually
has multiple different codons that encode it.
So you could have a single base change
and actually have no change whatsoever
in the amino acid that it's encoding.
All right. See, it's all starting to come together.
Hopefully, you're starting to see that,
that all the hard work you put into learning the material
in the first couple of modules
is starting to come back around now and be reinforced.
So that's the idea anyway.
Okay, so the next type of possible effect of a SNP
will be a missense mutation, a missense.
So again, there's some funny words in genetics.
We talked about the antisense strand.
This is a missense mutation, and missense,
it means a results in one amino acid change in the protein.
So let's take an example of that CGG sequence,
instead of it being changed to CGT,
which was coding for the same amino acid.
Let's say that the mutation was changing
that first C to a T, so now it's A TGG.
This would change the protein from having an alanine in
that location to having a threonine.
Because if you look up on your chart, you would see
that a CGG codes for alanine, but a TGG codes for threonine,
which is a different amino acid,
but would only affect that one
where the mutation is located.
And this may have an effect on the phenotype,
by possibly changing the protein shape
and therefore its function.
And certainly there are diseases as we already talked about,
sickle cell disease, is the result
of a single amino acid being changed.
Now, that's not the case for most amino acids.
I'd say in most proteins there's a little bit of flexibility
in terms of their functions,
so being maintained even if there's a single change.
But there are those very specific amino acids
which are really important to have the right ones there.
And so missense mutations can actually cause
or lead to certainly disease.
A nonsense mutation results in a truncated protein
because of the creation of a stop codon.
So let's take the example of our original, our wild type.
Remember our wild type sequence is TTT,
and that this is now mutated to ATT,
which would result in the ribosomes reading a stop signal
instead of a lysine.
So none of the codons following this mutation will be read
or translated resulting in a shortened protein.
So TTT codes for lysine, and what you would normally have,
let's say this was part of your mRNA sequence.
Well rather, let's say this is part of your DNA sequence,
it gets transcribed right into mRNA.
So the mRNA would read UUU,
and the ribosome would read that and say,
okay, that's a lysine,
and then it would move on to the next codon
and move on to the next, and move on to the next,
move on to the next.
Well, in the case of a nonsense mutation,
that changes the codon from a codon
which would normally encode for an amino acid to a stop.
So now the ribosome gets to that sequence
and says, oh, that means stop and it falls off.
And the problem is not only do you not translate
or incorporate that particular, in this case,
lysine into the growing protein chain, you also
don't continue on with reading the rest of that mRNA.
So anything downstream or that comes after that new mutation
or that that nonsense mutation doesn't get read.
And so the protein basically is short or truncated
because none of the rest of what comes after,
is now a stop codon, gets read by the ribosome.
So this can be a big, big problem. And it, and it often is.
So if there's a nonsense mutation that happens,
basically a protein will be either very, you know,
have a severely reduced function to it,
or it will actually be completely non-functional whatsoever,
which can be a real problem
and can certainly lead to disease.
Let's take a quick peek at what I'm talking about here
so you can see it more visually here, silent mutation.
And let's just orient ourselves to what we're looking at.
On the top here is the DNA template strand.
So that would be the two strands,
and the mRNA that gets transcribed off of that.
And then the protein, the amino acid sequence,
which gets read.
And again, you can go back to your amino acid table
to confirm that this is what it basically would read.
But let's say that this is the wild type.
Again, remember wild type or normal functioning sequence.
And here you have the, the normal, let's say,
I mean this would be extremely short word protein.
This is just for demonstration purposes only.
Normal proteins are, I think, in the range of at least,
3, 400 amino acids usually.
So they're much, much longer than this.
And some of them are, you know,
even in thousands of amino acids long.
But let's just look at this,
this is just for demonstration purposes.
You have your methionine, lysine, phenylalanine, glycine,
and then it reads this stop codon here.
Well, in this case, let's say that the guanine here
was mutated to an alanine, so an A instead of a G.
So this gets read as GGU, but that still codes for glycine.
GGC and the mRNA and GGU both code for glycine.
So this is a silent mutation.
There's no change in the amino acid sequence,
so there's no change in the protein whatsoever.
So there's no detriment to this.
Okay, a missense mutation, let's look again,
same type of sequence that we were looking at
in the previous slide.
Here, let's say instead of the C in this location
and the wild type strand, rather,
there's now a T, so a T instead of a C.
And what does that change?
Well now, instead of it being GGC in the mRNA,
it's now AGC, which is a codon which encodes for serine
as opposed to glycine.
So there is one amino acid difference in this protein
as a result of a missense mutation.
So silent mutations are really, you know,
not going to have any effect whatsoever on a person.
A missense mutation, very specific ones,
can have detriments to a person,
but generally they're more tolerable
because it's a single amino acid has been changed.
And unless that amino acid is in a really important location
for the protein, then the protein and overall the cell
and therefore the individual might be able to tolerate
a nonsense mutation.
A nonsense mutation, this is the one that results
in the truncated protein because you're now creating
a stop codon earlier on in the chain, right?
Remember because it gets read just like you're reading
a sentence from left to right.
The ribosome is also reading the mRNA from left to right.
So as soon as it hits what it reads as a stop codon,
it stops, the ribosome falls off, and the protein is done.
No matter what stage it's at, it doesn't keep going
because it reads that as a stop codon.
So in this case, instead of the T located here,
this is now mutated to an A
and this gets read as a UAG in the mRNA.
And so, basically, the protein stops being formed
right here, and there's really nothing to it.
It doesn't have the meat of the protein.
So any amino acids that would be encoded,
any past this stop codon,
just will never see the light of day.
They'll never be read by the ribosomes,
'cause the ribosomes reach that stop.
'Cause again, remember, they're moving left to right,
they're sliding along, read three, move up, slide along,
read three, get up, move read three.
But here it reads three, it puts methionine,
it moves over to the next three and it reads,
oh stop, our job's done, you know, it's quitting time,
and the ribosome drops off and that's it for the protein.
It basically doesn't get any more amino acids added onto it.
All right, let's think about insertions and deletions.
So there's a couple of different effects that can happen
and these tend to be more severe.
So when there's an insertion or a deletion,
these tend to be more severe
and we'll talk about why in a moment.
More severe than a point mutation or a SNP.
So an in-frame insertion, this would be one or more
complete codons inserted without disrupting any
of the existing codons resulting in
one or more added amino acids to the protein.
Okay, that's a lot of words
and I'll show you visually what this means in a moment.
So just hang with me for a second,
just wanna get a few definitions out of the way.
An in-frame deletion would be deleting one
or more complete codons without disrupting any
of the existing codons, which results in
one or more amino acids removed from the protein.
Okay. So remember before when we were talking about, say,
a missense mutation, which would be changing
one amino acid to a different amino acid.
In this case where with in-frame insertions or deletions,
you're adding one more amino acid
or taking away one amino acid.
It's not that you're changing one,
you're just adding one or you're taking one away.
A frame shift insertion or deletion,
which is actually the most likely kind of insertion
or deletion results in all codons following the insertion
or deletion of one or more bases.
And that disrupts the codons following the insertion
or deletion to be incorrect.
So all of the amino acids in the protein coded for
after the mutation will be incorrect.
So that means all the triplets are off by one or two.
And as you can imagine, that's a real problem.
Let's take a look at that.
But first, let's take a peek at the in-frame
insertions and deletions.
So in-frame versus frameshift,
frameshift is bad news for the protein.
It really, really is.
So let's take a look at why that might be.
And if you think about this,
I've used the analogy of thinking about reading an mRNA
as if you were reading words in a sentence.
The order of the letters that compose the sentence
are very important.
And it's also important where you put the spaces
between those words.
And that's kind of like thinking
of the letters in the words being like each base
and the space between them being like reading one codon
versus the next, versus the next.
So if in the wild type, let's say that the wild type
would be like the sentence.
So we're using sentences made up of three letter words
because it's sort of like the three base codons, right?
So each letter is like a base
and each word here is like a codon, okay?
And let's say that the sentence is like the protein.
All right. So if we were reading the wild type,
let's say the wild type sentence is,
the red bug bit the dog.
For an in-frame insertion,
we're adding in another three bases,
say we're adding in, basically, one additional codon.
So it would be inserting three bases and it doesn't change,
basically, adjust how the rest of the codons are read.
So in this case it would be like adding the word top.
So now it would be, the red top bug bit the dog.
So that's a little bit different
than the wild type sentence, so the red bug bit the dog.
Now it reads, the red top bug bit the dog.
So that might make a difference in terms
of the proteins function.
An in-frame deletion would be like removing one of the words
or one of the codons.
So now it would read, the bug bit the dog.
So you're missing some information here, right?
So before it was, the red bug bit the dog.
Now it's just, the bug bit the dog.
So we lost red,
but you can still kind of understand the sentence.
It still makes sense.
It's still providing you some information,
just a little less.
So most likely an in-frame deletion like this,
that's especially one that's just deleting a single codon
would really probably not have a dramatic impact
on the protein's function.
However, if we start messing around with the frame
of how the codons are read,
here, you get into some trouble.
So a frameshift insertion.
So let's say we're adding in a single nucleotide.
Let's say in this case you're adding a single base,
and this is our analogy of using letters instead of bases.
So let's just like adding the letter F into
the sentence that we had before.
But you still have to read each of these in groups of three.
So now it would be THE REF DBU GBI TTH EDO G.
Okay, that doesn't make any sense, right?
I mean you still get the word the,
that kind of makes sense, that's fine.
That's just the same.
But anything that comes after that frameshift insertion
gets all totally screwed up.
And now the ribosomes are reading these codons
which are now all off by one,
which totally screws it up
because now when it goes to read that,
it's coding for completely different amino acids,
which means the protein's totally different.
It makes no sense.
The same thing is true for a deletion,
let's say deleting a single nucleotide.
And again, we're demonstrating that
through taking out one of the letters.
Now what it would be is THE REB UGB ITT HED OG.
Yeah, that doesn't make any sense either.
Same thing with insertion for a frameshift deletion,
you know, anything that comes after
where that deletion occurred doesn't make any sense anymore.
And now the protein's totally different,
probably loses its function altogether
or starts doing something crazy that it shouldn't be doing.
And this can definitely lead to disease.
Let's take a quick peek at what we're talking about here.
So in-frame insertion, here you have the wild type sequence,
the DNA sequence on the top in blue,
followed by the mRNA sequence in red,
and then the protein sequence, and I'm writing that out
as the three letter designation for each amino acid.
So this is our wild type sequence.
Then an in-frame insertion means we're adding exactly
three bases or a number divisible by three number of bases.
And you're also maintaining the frame.
So here we're adding in a TCT, let's say,
or an AGA right in between codons two and three.
So basically now our protein,
what does our protein look like?
So methionine, glutamine, now there's an arginine,
and then it's followed by the rest of the, you know,
the regular sequence of the protein,
cystine, proline, proline, leucine, glutamic acid.
All right. So the protein has one additional
amino acid as the end result.
Similarly for deletion, it's basically like
taking out exactly the three nucleotides,
which would encode for a single codon.
So nothing gets shifted around,
but you have one fewer amino acid there.
So now we've lost our cystine.
And so it's methionine, glutamine, proline, proline,
leucine, glutamic acid, and the cystine is now gone.
So this can have an impact on the protein certainly,
but it's not totally screwing everything up.
Now if we wanna start screwing stuff up,
let's take a look at what a frameshift insertion would do.
What would insertion do?
Well, let's say we're just adding one nucleotide.
Like what can that hurt, right?
Just putting one base in those.
Those other two examples, you're adding three bases.
Shouldn't that have a bigger impact?
Well, no, because it totally changes
and shifts the way the ribosomes are reading
those triplets of bases,
which is so important, so important.
So one little base off and everything gets screwed up.
Just like those words in the sentence
that we were just talking about.
You shift things over one to the left or one to the right
and it doesn't make any sense anymore, right?
It's gibberish, and that's kind of what happens
to the protein.
So let's take this example.
We're adding an A here and so everything
basically gets shifted over to the right by one
as far as how the ribosome is going to read the sequence.
So now the ribosome reads AUG, yep, same as before,
CAA, yep, same as before,
but now it's reading AUG, which is methionine, not cystine.
So it basically has totally shifted over by one.
So instead of reading it the normal way it's supposed to,
now everything gets basically shifted over one.
So now instead of reading TGT, CCG, it's now going
to read TCC, GCC, see what I'm saying?
ATT, and that's what you have down here.
All right. And that results in completely different
amino acids being read after the frameshift.
A deletion, same thing.
You just taking out one little base.
What can that hurt?
Well, there's a lot
because now everything gets screwed up after that.
And again, same thing.
So let's say we're removing this T here,
so everything moves back over this way one.
So everything gets moved over one again,
and here you have the same problems.
All the amino acids following that frameshift
are completely different.
And then the protein gets totally screwed up.
So as you might be able to start imagining,
since it's everything that follows that mutation
gets screwed up, the closer to the start codon
that a frameshift mutation happens,
the more detrimental it is to the protein.
Similarly, the closer to the start codon,
the start of translation that a nonsense mutation happens.
So basically changing a codon for an amino acid
to a stop codon, the closer that happens to the start codon,
the more screwed up the protein's going to be
'cause the shorter the protein's going to be.
Same thing here in a frameshift,
the closer that mutation happens to the start
of translation, that means all of the amino acids
following it are going to be screwed up,
so the worst it actually is for the protein.
Okay, let's talk about a little nomenclature
for mutations which result in changes to the protein.
So this is definitely not all of it.
Unfortunately, it's not all totally standardized,
so you might see this in different ways.
I just want to give you at least one way
that you might start to see some of these.
I'm not going to go in a lot of gory detail here
'cause it gets to just be like a lot of memorization
and it's not totally necessary.
I just want you to, when you see something, say, on a chart
or, you know, in a test result or something,
I want you to be able to recognize it at least,
and then you can kind of look up what it means,
specifically in that context.
But to give you a sense of what you might see.
The nomenclature likely denotes the changes
in the amino acid sequence, not the DNA sequence.
And they may use a single letter
or the three letter amino acid designation.
As you saw I was using the three letter
amino acid designation, but there's also single letters,
which is what I have down here.
And you can look those up just as you can look up
a table of that online, you know, for the 20 amino acids,
what the single letter and three letter designations are
for each of those.
For a nonsense mutation, it's designated as
the amino acid which is changed at its location
along the chain of amino acids,
and it's followed by the letter X.
And that X basically means its stopped.
So nothing else follows that.
So in this case we have G542X.
If you see that, then you know that it is the glycine,
which is the amino acid which is designated by the letter G.
Glycine, at the 542nd amino acid in the chain of amino acids
for this protein, is normally a glycine.
So the wild type is glycine.
But now in this individual who has nonsense mutation
that it is now a stop codon.
So it is designated as an X because no amino acids
have X's there as single letter designation. Okay.
And missense mutation is designated by the wild type
or the old amino acid, you can think of it that way.
It's location, and then the new or mutant amino acid,
that's now in its place.
In this example would be glycine at location 176.
So the 176th amino acid in the chain is no longer glycine.
It's now F which stands for phenylalanine. Okay.
And in-frame deletion is denoted by a delta
or could be denoted as the letters DEL for deletion.
But you may see it as the delta symbol,
then the amino acid, which is deleted and its location.
So this would be a deletion of the phenylalanine
at location 508 in that particular protein.
And in-frame insertion, here's where we're supposed
to get a little ugly with in-frame insertions and frames.
It just gets really hairy with how it's designated
and it's designated different ways depending upon,
I don't know, what the person ate
for breakfast that morning.
There doesn't seem to be a lot of rhyme or reason
to it sometimes, but here's at least one way
in which an in-frame insertion can be denoted.
It would be denoted as the amino acid before
and the amino acid after.
And so it would be denoted as the wild type,
which would normally be leucine at location 21,
followed by a lysine at location 22.
And there's an insertion now of a three ins.
So in this individual if you were reading
their amino acids in this protein starting at amino acid 21,
would read as leucine, threonine, lysine,
and then all the rest of the amino acids
are in the normal order
as you would expect for this protein.
Frameshifts, it gets more complicated.
But if you see the letters fs in the designation,
that means there is a frameshift at that location
that they are specifying.
But again, yeah, it gets a little weird.
I still haven't quite figured out if there's...
it doesn't seem like there's a standard way to do it.
So if you see the letters fs,
that likely means it's referring to a frameshift.
And I apologize, I can't give you more direction than that.
It's just I've seen it so many different ways
that it would really, I think, be a waste of time
to try to go through all of them.
But anyway, if you see those,
at least you'll be familiar with what those may indicate.
All right, let's move on to some categories
of genetic disease.
Chromosomal disorders, which we talked about a lot
in the last module.
These are polygenic, and by that I mean they're involved
with multiple genes and that would be all of the genes
in the chromosome, if it's aneuploidy.
Basically, the disorder itself may be
the phenotype of the disorder.
So let's say the phenotype would be down syndrome.
The genotype would be trisomy of chromosome 21.
So the phenotype would be the characteristic,
which would be down syndrome,
all that's associated with that.
The genotype would be what caused it
from a sequence perspective.
And that would be a trisomy of chromosome 21.
So chromosomal disorders are polygenic, right?
So they involve many different genes,
however many different genes are either on the chromosome
itself, if it's an aneuploidy
or in the region where there's a chromosomal disorder.
And that contributes to all of the different
and various symptoms that you see associated
with chromosomal disorders.
A single gene disorder would be considered monogenic.
There are over 6,000 different identified disorders
that fall into this category.
They're often called Mendelian disorders as well.
You might hear that,
we'll talk about that a lot in the next lecture.
And then there are multifactorial,
which is nearly all diseases to varying degrees,
which could be considered multifactorial,
which means they are involved with multiple genes
to different extents and influence from the environment.
We'll talk about this in the next module.
And those would be diseases like cardiovascular disease.
Cancer, for example, is also
a multifactorial genetic disease.
You know, stroke risk, all of these are multifactorial.
Chromosomal disorders, as you recall,
these would be either a full on aneuploidy
or it could be a portion of a chromosome is deleted,
duplicated, inverted, transferred from one chromosome
to another, you remember all of those
from the last module, hopefully.
So this is excess or lack of a whole chromosome
or segment of a chromosome.
So phenotype is the net effect
of changes in many different genes. Okay.
Single gene disorders, these would be disorders
like cystic fibrosis, which occurs when both copies
of the CFTR gene are mutated.
And we will go into that in the next lecture.
This would be a mutation or disruption in a single gene
which results in the disease.
So for a person who has the genotype
which determines cystic fibrosis,
it doesn't matter what that person does, right?
So they could live the healthiest life they possibly could,
they're still going to develop, at least,
some of the symptoms of cystic fibrosis.
They're still going to develop cystic fibrosis
because getting that particular disease,
the manifestation of that disease is 100 percent
determined by the genotype for the cystic fibrosis gene.
So it's monogenic, single gene influencing it,
and in particular mutations in that gene
will give you the disease.
The disease will absolutely manifest.
As opposed to multifactorial disorders,
where you can have really a combination of effects.
And again, this is most of what you see,
certainly on a day-to-day basis.
And this will be most diseases are
influenced by many different factors.
So if you take hypertension for example, well as you know,
right, that's going to be influenced dramatically by
a person's diet, by whether they smoke or not,
by their lifestyle, so whether they're sedentary
or do regular amounts of exercise.
But it's also influenced by a variety of different genes
and different mutations in those genes.
They all contribute a little bit to the risk associated
with potentially developing something like hypertension.
Okay. Yes, and hypertension involves over 15 genes
as well as diet, exercise, and smoking exposure.
And we'll get into a little more of that in the next module.
These become a lot more difficult to nail down
and give, you know, precise estimates to patients
as far as what's their risk because there are a lot
of factors contributing a little bit of risk.
And it's really the combination of those
that will determine whether or not
a person develops a particular disorder
and the extent to which they do.
All right, let's summarize here.
Genotype leads to phenotype.
So your genotype would be the sequence of a particular gene,
and that's going to lead to the phenotype
or how the genotype is seen in an individual.
So their traits are affected by a particular genotype.
Changes to a gene sequence can result in changes
to the protein it encodes, which can affect phenotype.
We gave you a few examples there of the sickle cell disease
and cystic fibrosis, how changes in those proteins
can affect the individual.
Mutations include changing a base or point mutation
or inserting or deleting one or more bases.
And these mutations can cause one amino acid
to be different, which would be a missense.
The protein to be truncated, which would be nonsense,
and amino acid to be added or removed,
which would be an in-frame insertion or deletion,
or the protein to be dramatically different,
which would be from a frameshift.
Genetic diseases can be monogenic,
polygenic, or multifactorial.
All right, so what's up next in this module?
Well, the remaining two lectures,
we're going to dive into patterns of inheritance
that are commonly called Mendelian Inheritance,
which means inheritance of conditions
that are caused by a single gene.
So looking at inheritance of a single gene.
And so we're gonna have two lectures on that.
The first one is on the basics of Mendelian Inheritance,
and that's where we get those terms of dominant
and recessive, I'm sure you're familiar with.
And then we're going to move on
to some extensions to Mendel.
So as we know all too well in genetics,
there's always exceptions
and some of them are actually pretty important to make sure
that you're familiar with and aware of
in things you might see in your practice
or patterns of inheritance that might not quite fit exactly
what we learned about from the Mendelian Inheritance.
So with that, I will say goodbye
and we'll talk with you in the next lecture.