Genetics - Lecture # 3

Wednesday 29-9-2010
Done by: Sara Al-Zu'bi 

The Bubble Boy Syndrome and The Structure of DNA

“Today, we will continue the last portion of the previous

lecture, we already talked about”:
 The different chemical reagents and drugs that are
used to interfere with nucleotide metabolism and how
important they are in interfering with the pathways; as they
are used for treatment of some diseases such as; cancer and
antiviral or antibacterial cells.

 And we saw some structures of the drugs <you are not

supposed to memorize them, just have an idea about the
similarity in structure between those agents and the
intermediates of nucleotides or the nucleotides themselves>.

Today, I will talk about a disease caused by the

deficiency of an important enzyme which is: Adenosine
Deaminase. Some people have this enzyme deficient. The
importance of this enzyme is to convert adenosine or
deoxyadenosine to inosine or deoxyinosine.

• When we have AMP or dAMP, we end with adenosine or

deoxyadenosine by nucleotidase, and we end up with
inosine and deoxyinosine by adenosine deaminase
(by deamination), then they will follow the scheme on
the next page to reach the uric acid, as we’ve seen in
GMP and UMP degradation.

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 • Some people have this enzyme deficient, and as a result
there will be accumulation of dATP.

» It was found that dATP is toxic to the cell, because it

inhibits the ribonucleotide diphosphate reductase
(RNDPR).

» The importance of this enzyme (RNDPR) is: The conversion

of ribonucleotides to deoxyribonucleoties, and this
conversion is important because it will give the substrates
for DNA synthesis, which are the four
deoxyribonucleotides.

 So, you block that enzyme because of the

accumulation of dATP, then the enzyme will be inhibited.

*** It was found that the immune system’s cells, which induce
the different responses in immunity, are highly sensitive to
dATP, as a result, the whole immune system will be blocked

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in those people >> Because of this, it is called SEVERE
COMBINED IMMUNODIFICIENCY DISEASE, or abbreviated
as SCID.
 As the doctor mentioned last time; it is called also
BUBBLE BOY SYNDROME. This deficiency was discovered in a
boy with a complete immune deficiency, so he was put in an
isolated environment in order to avoid infections >> that
deficiency in the immune system is a result of adenosine
deaminase deficiency.

What is interesting about this disease is that they tried

the first level of gene therapy for the treatment of the
disease -that was before 15 to 20 years from now-, BUT it
didn’t succeed. They tried to introduce the adenosine
deaminase to the patient, but nowadays they are using the
stem cells so they could introduce the healthy enzyme or
the gene of the enzyme, so the disease could be cured by
this technology.

** The doctor showed us a patient who is in an isolated

environment because of the immune system deficiency. BUT
that picture isn't found in the slides!!

SO, we are done with this part of the lecture and now we will
transfer to the next topic concerning this course
………………………………………  
We are going to talk about the DNA structure, genes,
chromatin, and chromosomes. These are the topics that we
will cover in this lecture and in the next one.

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 Lectures 3 & 4
DNA, Genes, & Chromatin

On slide 1, the objectives that will be covered today which

the doctor wants us to know.
<< I hope that you have reviewed the specific objectives for
lectures 1 and 2 and you didn’t find any difficulty or problem
in understanding them >>

The same thing here, you have to -after we finish these 2

lectures (3 & 4) or during discussing them- ask yourselves
about these specific objectives if you understand them or not.
So we are going to talk about:
- The building blocks of the DNA in terms of; structure,
the bases, nucleosides, nucleotides and the double
stranded DNA.
- A little bit about the structure of the DNA, the base
pairing, the complementarity, & the antiparallel.
- Some physical characteristics of DNA in terms of the
kinetics of disassociation or regeneration of DNA
because that will help you to identify the different types
of DNA.
- How this HUGE molecule of DNA is packaged in a very
small size to be in the safe side to the nucleus.
>> DNA is a huge molecule which has a big size that the
space where it is located is much much much much
smaller than the size of this big molecule.
- Chromosomes and some structures of those
chromosomes.
LET'S START ………………… 

Genetic Dogma:
You know that the genetic diseases happen because of
mutations in a gene or mutations that affect the repair

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system of the mutations (means that there will be a mutation
in the gene because our DNA is always subjected to changes
and mutations through time, because of the environment and
the chemicals that we are exposed to).

>> So our DNA is always subjected to mutations or changes,

so there must be a mechanism in the body which is the
REPAIR MECHANISM that will fix and repair any mistake or
any mutation in the DNA.

Supposedly, those genes or enzymes -that are responsible for

repairing the mistakes- also have mutation >> then the
repair system will also be blocked.

SO a genetic disease will result because of a mutation in

the gene that repairs it. Also the genetic flow (the
information of the genetic constituents) will stop from one
generation to another because of those mutations or when
the repair is not replaced.

The flow of the genetic material:

The flow of the genetic material, as you can see on the next
page, the genetic material flows from DNA to DNA by DNA
replication (this means that the genetic material is produced
and transferred from one generation to another via DNA
replication or DNA synthesis).
 From DNA to RNA when a gene is expressed by a
process called: transcription process.
 From RNA to protein in order to have the proper
phenotype of the genetic character.

So, it starts from the DNA (or from the gene) in order to
conserve this genetic information. DNA must replicate,
so the genetic flow went from DNA to a new DNA via
replication. And DNA to RNA via transcription, in order

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 for the genetic traits (or information) to be transferred to
the protein. mRNA must be translated into protein, and
the protein will be processed in order to give the proper
function for the cell or for the organism, so this is how
the genetic material flows.

>> This flow of genetic information is called THE CENTRAL

DOGMA of MOLECULAR BIOLOGY, and the components of the
central dogma of molecular genetics are:
 DNA to DNA, DNA to RNA, RNA to protein 
Question: Is there any genetic flow from RNA to DNA?
 The answer: There is, sometimes, a reverse genetic flow.
Some viruses, in order to keep transferring the flow of the
genetic material, RNA must be converted into DNA by a
process called reverse transcription. And there are
enzymes responsible for this reverse transcription.

Question: Is there any genetic flow from protein to DNA or

RNA?
 The answer: Till now, it is not clear if there is any flow of
genetic information from protein to DNA or RNA, but in future
there might be something discovered. So far, some enzymes
(which are proteins) work back on other enzymes to modify
RNA, so this could open an area to start looking if there is any
genetic flow from protein to DNA or RNA.

NOW, we will talk about the DNA structure and its chemistry,
and in this aspect we will talk about some evidences that the
DNA is the genetic material, not protein or any other
compound.
>> SO, we will talk about: ¹DNA transformation and some
experiments to do that, ² transgenic experiments (that also
will give us evidence that the genetic material is transferred
via DNA), ³ some tools of mutations on some genes and look

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if the phenotype will be changed after we change the
genotype.

* NOTE: The phenotype is the appearance.

The genotype is the genetic constituents.

Question: What are the evidences that the genetic material

is the DNA (The molecule that transfers the genetic
information from one generation to another is the DNA)?
 The answer: There are 2 famous experiments done in
vivo and in vitro:

In vivo: They took specific bacterial cells (streptococcus),

and then some of the virulent bacteria were heat-killed (this
means they are not infective agents anymore), the other
group of cells are viable but not virulent (not infective
agents). And then they injected a mouse with these two
bacterial populations.
So we have 2 types of bacterial cells: heat-killed virulent
bacteria, and viable non-virulent bacteria.

>>> When you kill the bacteria, you kill all the enzymes and
proteins and every other infective agent.

What do you expect as a result? When the mouse was

injected with these two types of bacteria what happened to
that mouse, was it infected or not?
The result: The mouse was infected. Why?

Few students answered, but the answers weren’t heard,

unfortunately, but I have written the doctor’s comment on
them:
1- Yeah, but you killed the virulent strain by heat, and the
strain which is not virulent is not an infective agent.

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 Although we have these assumptions, the mouse was
infected!
2- Yeah, but it needs some components from the virulent
in order to replicate, so it will replicate but the result of
this replication is non-virulent, and why do we need
some of those components although it could replicate by
itself?! It’s a good explanation or conclusion, which is:
the other components in the heat-killed virulent bacteria
don't help the non-virulent to do any new thing.
3- (The correct answer) yeah this is exactly what happens,
although the effective strain was heat-killed but still the
DNA is there, and the DNA was mixed with the DNA of
the non-infective, and thus produced microorganisms of
the virulent that caused death of the mouse.
What happened is a transfer or mixing of the DNA
which carried the infectious character.

>> So, this is an evidence that the DNA is responsible for the
transfer of genetic material (this is in vivo).
In vitro: They looked at another two strains of bacteria with
specific phenotypes in vitro in a test tube. Suppose we have
strain A, which has a smooth colony -for example- and
another strain which has a rough colony. The smooth-colony-
producing-bacteria were killed and mixed with the rough-
colony-producing-bacteria and the result was: The rough
colonies have grown, although the rough colony was mixed
with the viable smooth colony bacteria.

So the genetic information was transferred from a specific

agent that was damaged but DNA wasn't damaged, so it
transferred the genetic information to the next generation.

Concerning transgenic experiments, you could introduce a

gene to an egg and look if that gene was expressed. You
could insert that gene in the ovum and the animal that is
produced after inserting a full gene in the egg is called a
transgenic animal.
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Transgenic animal: is an engineered animal in which a
foreign gene is introduced in the ovum and then the fertilized
egg grows, and the produced organism is called a transgenic
animal.

NOW, what they did with these transgenic animals is that

they started to look at some …. (the doctor was interrupted),
when they put the foreign gene, they changed the genotype
and they noticed that the phenotype has changed, for
example: if they insert a gene of a growth hormone in a
transgenic animal, they noticed that the transgenic animal
now is growing in size and volume, it is bigger than the
normal one which is not transgenic or the foreign gene wasn’t
inserted in.

So, this is another evidence that proves that the DNA is

responsible for changing the phenotype when the genetic
constituent is changed.

Another thing that was built in with transgenic animals, if

they want to study the effect of specific gene on a specific
character, they destroy that gene and start looking at the
phenotype of that new organism, that type of experimental is
called knockout transgenic animals, (Knocking out a
gene will produce a knockout transgenic animal).

This is also an evidence that DNA or part of the DNA will

change the phenotype because the genetic constituent was
changed.

Now, also another evidence that DNA is responsible for

changing the phenotype or transmitting genetic information
from one generation to another is the mutation that we have
in our DNA.

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If we look at each other we will not see any two individuals
looking the same except in identical twins, and they will also
have some little differences.

>> this is an evidence that the genetic information is

transmitted from one generation to another or the phenotype
is different because of something in the genetic constituent
has changed in the individuals due to mutations (and
mutation happens only to genes or genetic constituents or
the DNA).

So because of the variation in the DNA sequence (i.e. our

DNA is polymorphic, if you look at the DNA sequence of any
two individuals, you will see some differences in some regions
of the DNA) we are not the same in tolerating a disease - for
example -, or we are different in tolerating a drug - for
example - because our genetic constituents are different from
one person to another, so a patient taking a specific drug,
that patient could improve using that drug, but another
patient having the same disease using the same drug could
not improve because of the variation of individuals in the
genetic constituent due to polymorphic sequences of our DNA
due to mutations.

» these are the three principal concepts concerned as

evidences that DNA is the agent responsible for the transfer
and conservation of genetic material from one generation to
another, and transmitting that information from one
generation to another (it's not protein, it's not carbohydrates,
it's not amino acids, it’s a DNA molecule that is responsible
for those things)….. Slide #8

And those evidences are:

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 DNA transformation
 Transgenic experiments
 Mutation alters phenotype

NOW, you are familiar with the structures of bases; purines

(adenine and guanine), pyrimidines
(thymine and cytosine).

 In the previous two lectures, you saw

how they are biosynthesized and how
nucleosides are also biosynthesized.
BUT, what concerns us is: The
modification of some nitrogen bases.

One of the important modifications that

happened to our DNA is the
methylation (specifically to cytosine).

So you will see (in our DNA): 5-methylcytosine which is a

modified N. base of cytosine.

Methylation is a very important mechanism to regulate

gene expression and control it (regulation is an important
mechanism to control a specific gene expression)
I.e. supposedly, if you want to stop expression of gene, the
rate of methylation of that gene will be increased; those
methyl groups will cover that gene and prevent other
enzymes to come and initiate transcription of that gene.
But, it was found that 5-methylcytosine is rich in the
promoter regions, (they are very important to control gene
expression & to control transcription).
 SO there are a collection of cytosines (C & G) >> they are
called hot spots CG islands. They are located or clustered near
the promoter regions (you know the promoter regions are the
principal region to control gene expression).

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 When those are methylated, the gene expression will be
decreased and when they are demethylated, the gene
expression will be increased.

 The danger comes if: 5-methylcytosine was

deaminated.
I.e. Our DNA is always exposed to modifications, like
methylation, amination, and deamination. All these chemical
reactions could happen to our DNA and among those is: the
deamination of 5-methylcytosine.

** If 5-methlcytosine was deaminated, it will be converted to

THYMINE.

Question: If 5-methlcytosine is converted to thymine, what

are the consequences for that?

The answer: Mutations. If mutations happen to our DNA, we

have the repair system to discover that mistake and
automatically change it and put the right base in the gene or
in the DNA. BUT in this case, our repair system will break
down; it will not discover that this thymine was 5-
methylcytosine, because thymine is not a foreign base to our
DNA, so the repair won't take place.

 If the repair doesn't take place, then we will have

mutations. Mutations caused by the deamination of 5-
methylcytosine cause lots of cancer types in our bodies.

 Modification by methylation is important, specifically for

the CG islands which are located near the promoter.
Amination will cause cancers and other disorders.

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NOW, look at the following picture… these are the
nomenclature of a nucleoside and nucleotide.

You can see the base and

the glycosidic bond (always the numbering of the nitrogen
base takes the priority; the numbering for the sugar will take
the primes).

REMMEMBER THAT:
The glycosidic bond will be between 1' and N9 of the
nitrogen base.
If we talk about DNA then the sugar is deoxy sugar
(deoxyribose).
When we have the nitrogen base + the sugar the
compound is called nucleoside >> it's not guanine it's
guanosine, it's not adenine its adenosine.
The Phosphate group is going to be esterefied at the 5' and
3' regions, and if the phosphate attaches then that nucleoside
becomes a nucleotide (or nucleoside mono phosphate or
nucleoside diphosphate or nucleoside triphosphate).

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The picture below (or in slide 14) shows how the
polynucleotide is formed; in the picture is what we call a
polynucleotide.

The DNA has two

termini. The
conventional
starting head of the
polynucleotide is
called the 5' end
and the last
nucleotide (the
other terminal of
the polynucleotide)
is called the 3' end.

They (the 5’ end and the 3’ end) are connected with each
other via 3,5 diester bond (or phosphodiester bond), so 3'
from the first one and 5' from the second nucleotide in the
phosphate, and the same thing repeated; another
phosphodiester bond, so they run from 5' to 3'.

5' end in most cases has a free phosphate group and the 3'
end always has free hydroxyl group (you will see the
importance of having a free hydroxyl group in this region for
the expression of any gene or the synthesis of the DNA or for
the transcription).

 You have to memorize: the phosphodiester bonds from the

5' and 3’. The 5’end is the beginning and the 3' end is the
end of the polynucleotide, glycosidic bonds, and if you want
to read a polynucleotide you have to read it from the 5' end
to 3' end not vice versa. 

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 The DNA was discovered in 1951-1953 by Watson & Crick.
They published a paper in nature saying: the DNA is a double
helical structure, and all those conclusions came from a lot of
experiments for many years in order to reach those
conclusions.

We are going to review some of those conclusions about

DNA double helical structure:
- They found that the DNA is found in a double helical
structure and they discovered that later on (Watson and
Crick found by another evidences that it's a double
helical structure).

- and after 10 years another scientist did an experiment

called x-ray diffraction, and found the solid evidence that
the DNA is found in a double helical structure, and
discussed it with Watson and Crick and improved what
they have estimated or concluded.

 They found that in the DNA strands there must be

base pairing; they found that the cytosine paired with
guanine and adenine paired with thymine.

 According to the accurate measures and figures that

they concluded in their experiments in x-ray diffraction,
they found that the adenine couldn't paired with any
other nitrogen base except the thymine, the same thing
for guanine and cytosine

 The base pairing takes place by hydrogen bonds (H

bonds form when we have two highly electronegative
atoms).

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  These side chains of oxy carbonyl and amino group
aren't found for NO reason!! Those side chains are
very important for the stabilization of the double
helical structure via the hydrogen bonding.

 For the A-T base pairing, TWO hydrogen bonds could

be formed, and for the G-C base pairing - according to
the chemistry of the structure of these nitrogen bases
- THREE hydrogen bonds could be formed.

 As a conclusion: DNA is a double helical structure with two

strands; each strand is paired to the opposite strand and they
are complementary to each other (in terms of A VS T & C VS
G). They are anti-parallel (one is running from 5' to 3', & the
other is running the opposite direction (from 3’ to 5’).

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There are different forms of DNA, depending on how much
border is found in that molecule, but the famous form is
called B DNA form.
• DNA forms are: B form, A form, Z form and other forms.
• These forms are different from each other in: ¹terms of
dimensions, for example in the B form: we have 10 base
pairs every turn, while in another form of DNA may be
the number of base pairs is less or more.

² the rise between the N base and another in the B form

has a specific dimension, but in another form that distance
is different, so it gives us different shapes of these different
forms of DNA.

Now, an important thing is the two structures: the major

groove (which is deep and narrow), & the minor groove
(which is shallow and wide).

The importance of these grooves is for

proteins or the enzymes that will Major groove
interact with the DNA, control the DNA
expression, then their binding to the
DNA must be specific according to
specific sequence, that enzyme (which
comes and bind to affect the control Minor groove
of any gene expression) must be able
to read that specific sequences to
bind there or not to bind there.

The Major and minor grooves will

provide a place for those enzymes
when they come to bind to DNA to
read the sequence in that region.

SO, the function of these grooves: is

to build for specific binding for those
enzymes or protein to read what
sequence they are looking for to bind
and affect the gene expression.
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Now, talking about the composition of nucleotides of the DNA,
always the A=T and C=G. <<This is the rule known as
Chargaff’s rule>>

* Human DNA nucleotide composition is different from

bacterial or viral DNA.

What stabilizes the DNA double helical structure?

• The presence of the double stranded is very important
for the DNA replication or transcription.
• In a moment, you saw how N bases are arranged and
how the backbone of the DNA is arranged: The backbone
which is outside (the backbone from outside is:
phosphate sugar) and the N bases are inside the double
helical structure.

The phosphate
sugar backbone
outside the double
helical structure of
the DNA

The N bases
inside the double
helical structure of
the DNA

The existence of N bases in this arrangement is a stacked

form (stacked y3ne fo8 b39’hom l b39’) that will produce a

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force that will stabilize the double helical structure and that
force is the hydrophobic force.

 The 1st important force that stabilizes the double helical

structure of the DNA is the hydrophobic force that comes
from the stacking of the N bases.
Another important force that stabilizes the double helical
structure of the DNA is the H bonding between the base
pairs, although the strength of the H bond is NOT sufficient
but because we have tremendous, numerous numbers of H
bonds so this collection of H bonds between N bases in the
double helical structure will stabilize the double helical
structure.
 We have two forces that stabilize the double helical
structure of the DNA are:
 Hydrophobic force that comes from the stacking of the N
bases
 H bonds between the N bases

NOW, in the phosphate sugar backbone, Phosphate is

negatively charged and near it sugar then Phosphate (which
is negatively charged) >>> so, that
will produce a destabilizing force for the double helical
structure that is: the repulsion of the negative charges
between the Phosphates, but in vivo, those negative charges
are covered or neutralized by positive charges from some
metals, such as: Na, K, or by some basic proteins which are
positively charged and rich with basic amino acids. SO this
covering with positively charged molecules will prevent the
destabilization process of the DNA.

FINISHED 
-------------------------------------------------

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 STUDENTS QUESTIONS
These are the questions of the students, some of them I
heard them clearly, but most of them unfortunately I
couldn’t :D

If you want to go over them, here they are and I advise you to
read them because they contain some information that may
come in the exam, and it’s still up to you.

The proteins or enzymes that will bind to the major or minor

groove will stabilize or destabilize the DNA?

The answer: They will bind to the negative charge, either in

the minor or in the major, 6b3an when there is a
transcription, there will be changes when the gene will be

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expressed, instead of being packaged to each other it will be
unwrapped and all the enzymes will be exposed.

** The positive ion makes stabilization and of course the

negative ion destabilization.

Is there a reverse transcription in animal cells??

The answer: They are mainly in viruses, but there are

processes in human being where we will see the reverse
transcription.

The prions microorganisms have ribose, so it has protein

not genetic material, so how it does it replicate?

The answer: there is no microorganisms that have only

protein, prions are proteins produced by sensitive
microorganisms, and they are not themselves
microorganisms, so these are proteins produced by
specific microorganisms not microorganism itself. It makes
cow madness disease.

What controls the regulation process? (A good question)

the answer: there are enzymes that will methylate DNA

and those enzymes and the gene responsible on those
enzymes, when we talk about transcription you will see a
lot of DNA-protein interaction, that will stimulate, for
example, the gene 4-methylase in order to stop the
transcription of a gene or it will stimulate the expression
of demethylase gene in order to stimulate the expression
of the gene.

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 • So, it’s a DNA-protein interaction that will control this
methylation.

If we have 20 nucleotides, how many phosphates we

have?

The answer: 20 phosphates, 1 free OH group, 19

glycosidic bonds.

I couldn’t hear :D

The answer: The stability doesn’t allow or the distance

between the double helical DNA structure don’t permit
because the H bond for it are linked so it doesn’t fit or
stabilize the chemistry of the double helical.

>> And another students asked about mutations I guess and

the doctor said:

- It’s a dangerous mutation to have the transformation of

cytosine to thymine, especially because they are located
on promoter regions.

I couldn’t hear :D

The answer: Histones: are basic proteins that are rich

in basic amino acids that will bind to the negative charge
and neutralize it.

They will bind to the negative charges either in the

minor or in the major groove, of course when there is
transcription there will be changes, when the gene is
going to be expressed the region will be changed, so
instead of being packaged on each other it will be
unwrapped and it will be exposed to the enzymes.

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 ‫تم بحمد الله و توفيقه‬

I would like to thank one of my best freinds who helped me as possible

as she could,,, i can’t thank her enought with words just THANKS..... 

And i can’y forget my elder sister who stood me alot,

THANKS ....... 

‫أسأل الله تعالى التوفيق والهداية للجميع‬.

‫أعتذر ان كان هناك اي خطأ مهما كان بسيطا ً و سامحونا على أي حال‬.

 Done by: Sara Alzubi 

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