dna genes & chromosomes - كلية الطب€¦ · the forces stabilizing the dna double helix...

DNA Genes & Chromosomes ومن أحياها

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GENETICS

الفريق الطبي

االكاديمي

DNA Genes & Chromosomes

DONE BY : Buthaina Al-masaeed & Yousef Qandeel

GENETICS


Page 1

T(0:44 min)

In the pre lecture we take about the back bone of the double strand of DNA

that are composed of phosphate group bound together by phosphodiester

bonds ,its covalent bond and in the center we have nitrogen bases that

bond together by hydrogen bond.

The two strand are complementary to each other that’s mean if the C in one

strand they must be G in other complementary strand of it ,and if the A the

must be T because the hydrogen bound between the complementary bases

are the must stable and strong bound ,if the HB between T and G it will be

weak unstable bound and the whole structure will be destroy.

C always with G ,A with T very specific ,

T(3:58 min)

Q from student >>what is the mean of 5to3 end in the double strand ??

the bound that are form between subsequence nucleotides is bound by

phosphodiester bound ,so how phosphodiester form?? Its form between

the 3 primary carbon atom of the sugar with the 5 primary of the next

nucleotide.

Always the phosphodiester bound that are form between nucleotide the

are in form 3 primary to 5 primary .

Each stander it has two end (begging and ending)

The begging always characterize by having the 5 primary (free phosphate

group ) while the end have free hydroxyl group .


Page 2

T(7:11 min)

The DNA it must be helix structure as we see and called (double strand

helix structure) in this form of DNA will be function just in this structure

(helically).

Because of this twisted they will be major groove (large pocket) and the

minor groove (small pocket),this groove is very important because in there

process of any activation process of the gen like replication transcription or

expression of the gene ..there must be proteins to interact with the DNA.

Those proteins must bounds very specifically at specific sit on DNA .

Because of the major groove proteins can go to those major groove and

according to the hydrogen bond there they could read the sequence of the

nitrogen bases ,if that sequence recognize by them in order to bond they

will be binds ,because the are very specific so for any protein to came and

binds it must first scan the region by binding to the major groove and

reading the sequence .

The same thing for minor groove same proteins also will bind there but the

bulk of proteins will bind to the major groove to affect the active process of

the gens.


Page 3

T(11:35 min )

There are 3 forms of DNA the most famous form is the B-form found in our

cell, and also we have the A-form and Z-form.

A-form was discover ( Rosalind Franklin) .

Why you have different forms of DNA??its according to sequence reference

and also to the environment where the DNA is found.

In most of the cases we have B-form and in genetic characterize which

each term is composed of 10.5 bases per and its twisted right hand also A-

form in right hand while Z-form in left hand ( opposite direction) .

As we see the Z-form is extended more than A-B form.

In some cases of the dehydration A-form will be form.

Z-form is important and act like a marker for regulation of gen expression,

its mean when its gen near to expression the A-B form will be in Z-form.

Z-form its zig zag form and its beating sequence of C and G.

Forces affecting the stability of the DNA double helix

• hydrophobic interactions - stabilize

- hydrophobic inside and hydrophilic outside

• stacking interactions - stabilize

- relatively weak but additive van der Waals forces

• hydrogen bonding - stabilize

- relatively weak but additive and facilitates stacking

• electrostatic interactions - destabilize

- contributed primarily by the (negative) phosphates

- affect intrastrand and interstrand interactions

- repulsion can be neutralized with positive charges

(e.g., positively charged Na+ ions or proteins)

T (15:49 min)


Page 4

The doctor here took about the forces ,this forces so important to stable the

double helix structure ex hydrogen bond,.

Phosphodiester electrostatic repulsion by negatively charged phosphates

along the DNA backbone destabilize the double helix.

hydrophobic interactions is between nonpolar in the ring of nitrogen bases.

stacking interactions between the nitrogen bases.

T(19:46min )

The forces stabilizing the DNA double helix can be overcome by

heating the DNA in solution or by treating it with very high or very low

pH (low pH will also damage the DNA, whereas high pH will simply

separate the polynucleotide chains). When the strands of DNA

separate, the DNA is said to be denatured (when high temperature is

used to denature DNA, the DNA is said to be melted). Because some

of the forces stabilizing the DNA double helix are contributed by base

pairing interactions, and because A-T base pairs have only two

hydrogen bonds in contrast to G-C base pairs which have three

hydrogen bonds, regions of the DNA duplex that are A-T rich will

denature first. Once denaturation has begun, there is a cooperative

unwinding of the double helix that ultimately results in complete

strand separation.

This slide shows base

stacking and charge repulsion

in the DNA double helix


Page 5

Now a day a lot of DNA sample use for genetic testing to diagnosed

genetic disorder (take blood sample from the patient and repair it

and we must take it away from high heat ).

Denaturation process in vetro is very important for reaction called PCR

its abbreviation for (polymerase chain reaction )

PCR in test tube you Denature the DNA into single strand and by

specific reaction synthesis a billion of double strand DNA after

Denature it also use primary to extend them according to single

strand DNA and specific enzymes.

DNA could be renature unlike proteins, if you remove heat, urea, PH

so the DNA will renature or anneal to each other.


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Electron micrograph of partially melted DNA

This is how the DNA looks like under the electron microscope and this

figure represent partial denaturation of the DNA.

This happens due to base composition, regions with high A-T composition

that has only 2 hydrogen bonds will "breath" first forming what is called

"breathing bubble" but the C-G rich regions because they have 3 hydrogen

bonds they will melt late.

Hyperchromicity


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Spectrophotometer: used to measure how much specific compound will

absorb light & at which maximum absorbtion.

When a solution of double-stranded DNA is placed in a spectrophotometer

cuvette and the absorbance of the DNA is determined across the

electromagnetic spectrum, it characteristically shows an absorbance

maximum at 260 nm (in the UV region of the spectrum).

Proteins absorb UV light maximally at 280 nm

If the same DNA solution is melted, the absorbance at 260 nm increases

approximately 40%. This property is termed "hyperchromicity phenomena".

This is due to the fact that single-strand DNA is more exposed to UV light

(more surface area exposed to the light)

We can draw this curve depending on hyperchromacity at different

temperatures.

As you can see here hyperchromacity increase when we increase the

temperature due to denaturation of DNA (melting) until we reach a point

where there is no further increase in hyperchromacity because the DNA

become single-stranded at this point.

The temperature at the mid-point of the melting curve is called

"melting temperature" or "transition temperature" ( Tm) and it is very

important to be determined when you are performing PCR reactions


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Each one of these curves represents a DNA from different species

with different Tm due to difference in base composition (the more the DNA

has C-G the more the Tm)

Alu sequences are an example of interspersed DNA the function of them is not

discovered but they will cause some genetic diseases and this will be explained later


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Our genes and all mammalian genes are composed of introns and exons

each gene has a 5' beginning that has free phosphate group and a 3' end

that has free hydroxyl group

Introns: are regions in the genes that does not encode for amino acids

Exons : regions in the genes that code for amino acids

dna genes & chromosomes - كلية الطب€¦ · the forces stabilizing the dna double helix...

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