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-Dr Ma’mon

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We have talked about sequencing techniques and how science have developed from needing 12 years to get the full human genome in 2007 to being able to sequence anybodies genome in just 2-3 hours nowadays.

Scientists used to say that 97% of the human genome is junk DNA but a new

paper came out in 2012 and it said that 50-60% of the human genome is

relevant.

The human genome can be divided into:

- inter-genic sequences - Gene related sequences - coding sequences (which are the ones that make proteins)

Repeated sequences: the same pattern of bases repeated several times.

Pseudo-genes : they look like genes but they aren't functional.

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Repeated sequences

-Repeated sequences make up about 51% of our genome

An example on satellite DNA is centromeres and telomeres.

Tandem repeats come one after the other kind of like

telomeres but smaller.

Dispersed repeats are repeated sequences that are scattered along the DNA.

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Macro satellites:

Regions of 5-300 bp repeated 10^6-10^7 times

Centromeric repeats (171 bp) unique to each chromosome (you make

chromosome-specific probes)

Telomeric repeats

Mini satellites(VNTRs):

20-100 base pairs repeated 20-50 times and are tandemly repeated.

They are very important in disease diagnosis they are called VNTRs (variable

number tandom repeats).

They vary according to individuals like while having it one the same

chromosome on the same site, someone might have it 35 repeats while

someone else might have it 25 repeats.

So the sequence itself is of no importance but the number of repeats is

Important.

:

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Micro satellites(STR):

2-10 base pairs repeated 10-100 times

Again the sequence itself in of no importance but the important thing is the

number of repeats.

STR: short tandem repeats

Polymorphism among VNTRs and STR

Remember we are diploid so someone might have inherited different

repeats from both parents which yield different patterns even among

siblings.

Here PCR is applied because VNTRs and STR vary a lot among people.

Primers are used to surround the repeats.

The result of the PCR is used in forensics and maternity testing.

We distinguish the results by using gel-electrophoresis (the longer the

repeat the bigger the DNA piece is and the less it travels).

We now use STRs instead of VNTRs because they give more variability.

-This video might make it easier https://www.youtube.com/watch?v=DbR9xMXuK7c

We might encounter 2 people with the same alleles for 1 STR that’s why we use more than just one STR to make the probability of mistakes much less .

EXP: Individual A has got 3 and 10 repeats (heterozygous) so he gives 2 bands while

individual B is homozygous for 6 repeats so he gives 1 band and this is what we call

genetic finger printing (like finger prints the likelihood of 2 people having the same

finger print is unimaginably low) so the likelihood of two people having the same

repeats is extremely low.

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Real life example:

In this example we have grandparents who give a daughter and the other grandparents

give a son and the two of them give a bunch of offspring we can see that we have (4)

types of this STRs (1/3/4/6) repeats and by using gel-electrophoreses we were able to

know what the genetic-finger print of each one is ( keep in mind that some of them have

the same finger print for this STR that is why we use more than one STR in forensics and

other fields of this application ).

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Single nucleotide polymorphism (SNPs)

A single nucleotide base substitution for another at certain locations in our DNA, so basically we have the same gene at the same place on the chromosome

but while some people might have a (G) at a certain place others might have a

(T).

The difference between SNPs and a mutation is that SNPs happen in more

than 1% of the population (keep in mind they are mutations but they happen

so frequently that they are considered kind of normal).

Remember that mutations don’t have to be harmful (actually natural selection is kind of based on mutations) like blue eyes they are caused by a mutation but aren’t harmful

SNPs might be:

- Linked

- Causative

- Aren’t relevant

Linked means that they just happen to exist when a certain pheno-type is present

(they don’t cause it)" they guide us to the diseases gene".

Causative means they cause a certain pheno-type (they might be coding or non-

coding) coding means they are present in the area of the gene that gives proteins

while non-coding means they don’t give proteins but they affect other regions

including (promoters) they don’t change the amino acids but they change the activity

of the genes.

They are important in many fields including "pharmaco-genetics" where people need

different doses of the same drug to get the same effect

https://www.youtube.com/watch?v=tJjXpiWKMyA

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Transposons (jumping genes)

Genes which can change their location on the chromosome

They are either: - DNA transposons(2-3)% of our genome - RNA transposons(retro) which give:

long interspersed elements LINEs

Short interspersed elements SINEs

When the disease is caused by a transposon it's mostly of viral origin

Most of them lost the ability to change location

Some of them have the ability to change their location

When they change location they might jump inside a gene a affect it

causing a disease or they might "jump" to a location which affects the gene

or they mightn’t cause anything if they are far enough

-The doctor didn’t really emphasize on the list of diseases caused by transposons

https://www.youtube.com/watch?v=IPILDcABRkI

Transcription

General information before we start :

A chromosome is a single DNA molecule (we have 46 of them)

Chromatin: it's a chromosome with its related proteins (histons)

A gene is a region of DNA needed to give a functional

RNA (rRNA/mRNA/tRNA)

-https://www.youtube.com/watch?v=hywRdDVR76A ***

Cistron: another term for a Gene

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When a mRNA gives more than 1 protein it's polycistronic and when it gives 1

protein it's monocistronic

In bacteria different regions of the same mRNA give different proteins (polycistronic)

Transcription:

Making RNA from DNA

In transcription we use 1 strand of the double stranded DNA as a template to

make RNA (we can use both strands for RNA synthesis but some genes need

specific strands)

The thing that decides which strand to be used are "promoters" (regions of DNA

that guide the RNA polymerase)

The mRNA that is made is complementary to the used strand

The strand used to make mRNA is termed (-ve) sense

The direction of DNA reading is 3' to 5' while the direction of mRNA synthesis is

5' to 3'

polysomes: it's when many RNA polymerases make mRNA from the same

gene at the same time

-https://www.youtube.com/watch?v=mQh5ku9dyJQ ** part 1

- https://www.youtube.com/watch?v=icUBgcwp8QE ** part 2