Download Slide num. Notes 1 Office hours >> 9 – 12 Tuesday , Thursday 1 – 3

Slide num.
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Notes
Office hours >> 9 – 12 Tuesday , Thursday
1 – 3 Wednesday
* we have talked about 4 types of macromolecules , 3 of them was polymers because they consist of
monomers … ( lipids is NOT a polymer )
* nucleic acids are polymers because they are made of monomers … and they are two types : RNA &
DNA
* the monomers are nucleotides
* the basic chemical composition consist of 3 components :
1 – sugar … a pentose sugar ( 5 carbon ) , and it’s either a ribose ( anomeric carbon is beta ) or a
deoxyribose
2- phosphate
3 – a base … purine or pyrimidine
* deoxyribose , depends on the presence of
a – H instead of – OH on carbon number
2 .. and this is a difference between DNA
and RNA
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* the nitrogenous bases, , they all attach to carbon number 1 .. but they differ in how this carbon
number 1 is attach to the bases
* there are two classes of bases :
1 – purines : are two ring structures ( small name .. long structure )
2 – pyrimidines : single ring structure ( long name .. small structure )
* carbon number 1 of ribose attach to nitrogen number nine of purines and carbon number 1 of the
pentose sugar attaches to nitrogen number 1 of the pyrimidens ..
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* the doctor want us to “ MEMORIZE “ and know the structure of nucleotides .. so we could be able
to differentiate between them …
( just look at the groups which surrounds the rings )
* these differences are important , because sometimes these bases are modified in a way that they
become different and produce a mutation and we called this genetic mutation , but sometimes we
have mutations which are not genetic and known as epi-genitc mutations , which means that the
base remains the same but it’s modified differently … and epi-genitic mutation exists in identical
twins , in such a small difference between them ..
* there is other types of nucleotides .. the 5 that we have talked about are the ones that exists in
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nucleic acid .. but we have other nucleotides , they are derived from the 5 that we have talked
about ..
* uric acid results in gout
*pseudo means fake of looks like
* the doctor want us to know the 5 nucleic acid structure … and for the other nucleotides we just
need to look at them
- example for a question :
“ in the exam , if the doctor gave us the structure of Hypoxantine … and he asked us to identify it ..
the chooses would be “ adenine , uracil , guanine , Hypoxantine “ so u just have to answer the
quesyion by exceclotion
* nucleic acids are acids because they have a phosphate groups which is negatively charged
* we should name nucleosides and nucleotides … but , what are nucleosides !!?
- they are molecules that have a nitrogenus base + pentose sugar … BUT don’t have a phosphate ..
* how do we name nucleosides ?!
- if it’s an adenine .. we say “ adenosine “ … if it’s guanine we say “ guanosine “ ..and so on .. ( just
look at the table in the slides )
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* number of phosphate group if it’s not specified in the name ( mono , di , tri ) it can be one or two
or three ( eg : AMP = adenosine mono phosphate )
* if you know the structure of the sugar , and structure of the phosphate , and structure of bases .. u
just put them together and you will have the name !!
- if the doctor bring one of these structures in the exam .. how can we solve it ( name it ) ?!
* first .. look at it !!! >>> OMG … that’s a nucleic acid :P
* does it have a phosphate ?! yes >> it’s a nucleotide ! no .. it’s a nucleoside !
* look at the sugar , at carbon 2 … if there is – H it’s deoxyribose .. it there is – OH it’s ribose
* look at the base … it’s purine or pyrimidine ..
*look at the number of phosphate
after all of this u should be able to name them > ( just look at the names and follow these steps )
* nucleic acid polymers …is a nucleotide attach to a nucleotide and soo on
* we should notice something’s :
- when you attach a nucleotide to another , you take the phosphate of carbon number 5 , and you
attach it to carbon number 3 … and if you add another nucleotide you do the same !
- you always have a 3 , 5 ends !
- nucleotide number one is near the 5 .. and the last one is near 3
* double helix : because u have two strands , that go around each other ( interline around each
other ) and helix because they have a helical structure ..
* back bone : phosphate and the sugar
* side chain : the bases , which are directed inside the double helix.
* antiparallel : because one strand goes 5 to 3 and the other 3 to 5
* specific base-pairing or chargaf’s rule : number of A = number of T … number of C = G .. BUT
number of A and T doesn’t equal number of C and G
*stable : very highly stable , but it’s flexible
* groovings : because the two strands don’t go around each other in a perfect manner .. they go
around each other in a sort of an angle .. and opposite to any major groove there is a minor grove
* DNA is stable because of the chemical interactions … and it has :
- covalent bonds
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- ionic interactions ( charge charge interactions ) , and the phosphate is the responsible for these
interactions.
- hydrogen bonds : A forms 2 hydrogen bonds with T /// G forms 3 H-bonds with C
- van der walls interactions : remember that we have the bases in the top of sugars , so there are
van der walls interactions between the bases and the sugars
- hydrophobic interactions : between the bases , because they are highly hydrophobic .. they are
stack in each other and this cause repulsion and as a result there is an angle and a twist …and
because of van der walls and hydrophobic interactions , the DNA has a helical formation …
* the DNA that was drawn by Watson and greag is known as B – DNA … and they said that it has a
major groove and a minor groove … and it’s right handed because it’s going In the direction of right
* there are 10 bases pair full turn ..
*they found that there is other forms of DNA , such as :
*A – DNA : is right handed // exists in solutions that are highly ionic or high salt concentration
and as a result of that , water is expelled and the basses are stacked closer to each other .. so the A –
DNA is more compact and it’s thinner .. and it has 11 basses pair full turn
*Z – DNA : zig-zag DNA // it’s left handed // exists when you have a sequence of repetitive purine
purmidine …
* DNA is packed in our nucleus ..
* how is DNA is packed ?!
- first you have the formation of an octomer …which means .. 2H2A , 2H2B , 2H3 , 2H4 .. they form a
unit of 8 proteins ( octa = 8 ! )
- then DNA is packed around it , and then you have several octomers and the DNA is also packed
around them
- the octomer + the DNA around it + the DNA that links one octomer to another … all of this is
known as Nucleosome.
- the function of H1 ( it’s not a part of the octomer ) … it stabilize the reaction between the DNA and
the octomer ..
* chromatosome = 5 classes of histones + DNA without the linker DNA
*histones and DNA interact by electrostatic interactions because DNA is negatively charged .. so
Histones is positively charged !!
*RNA is single stranded
*contain uracel instead of thymine
* it can also form secondary structures .. by ‫ يلف حولين حاله‬forming H-bonds like : tRNA
*transcription : synthesis of RNA from DNA .. forming mRNA which localized in the nucleus and then
transported to the cytoplasm , where it’s translated into protein ..
*so inside the nucleus we have transcription ..
* outside the nucleus we have interaction of different types of RNA molecules ( mRNA , tRNA ,
rRNA )
- tRNA .. add amino acids /// - rRNA : exists in ribosomes
*mRNA have different sizes , depending on the size of the gene .. so if the gene is large the mRNA
would be large and so on ..
*mRNA is modified by removing the entrons and keeping the exons in the nucleus .. and then the
mRNA is transported out to the cytoplasm
* tRNA is single stranded .. and it has secondary structures ( H-bonds)
We should know them
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* there are other types of RNA molecules that exists in cells , and they have very important
functions .. and they are :
- snRNA : help modifying the mRNA by removing the entrons ..
-miRNA + siRNA .. they regulate synthesis of proteins from mRNA
* one features of nucleic acid is that it can absorb light … but the light it absorb is at a wavelength
of 260 nm which is Uvi wave length and we can’t see it
* if we have a sample of DNA .. and this DNA absorbs a unit of 1 .. this means that the concentration
of DNA in this sample is 50 micrograms/ml of DNA is needed to absorb one unit of light
*which one absorb more light .. single stranded or double ?!
- single stranded .. because u need a less of it to absorb the same amount of light
*DNA can be denature : we have 2 strands of DNA , and they are attach via H-bonds which are weak
bonds and can be broken easily .. if we increase the temperature , these bonds are broken ..
* so denature means : separate the two strands
*renaturation : if we lower the temperature the two strands will come back together
*if we have a double stranded DNA and absorb light at unit of 1 … and we increase the
temperature .. the DNA will start to melt and denature into single stranded DNA , which would
absorb more light than the double stranded DNA ..
*melting point : it’s the temperature where 50% of the double stranded DNA is melted into single
stranded DNA
*melting point depend on a number of factors and we will focus on the first one .. G- C content ..
which means , how many G-C we have ! because G forms 3 H-bonds with C ..
*it require higher tempreture to denature a douple stranded DNA with more G – C than a double
stranded DNA with less G-C ..
* the melting point for a higher C-G content would be higher
done by : omar sawas
sorry for any mistakes ^^”