LEC 1 :
Slide num
Slide 9 : slide 14 : slide 19 : slide 24 : slide 25 : slide 26 : slide 27 : slide 28 : slide 30 : slide 31 : slide 32 : slide 34 : slide 35 : slide 39 :
Notes
- molecular biology is biochm , but deal only with DNA.
- biochem = chemistry + biology
- K and Na , used in nervous system
- Fe used in blood
- ionic bond : total donation and total acceptance
- covalent bond : sharing of e-
- variable geometry leads to 3d structures
* there is no triple bonds in our systems in our body
- shorter = closer
- stronger = more energy
- double bond can’t rotate
- polarity : a part of atom have partial + , and other part have partial -
- depend on electro negativity ( ability to attract e- )
- Carbon is intermediate , does not attract e-
- add hydrophobic interactions
- electrostatic interactions = charge-charge interactions = ionic interactions
- in ionic bonds there is donation and acceptance for e- … but in ionic interactions the reaction is between charges
- hydrogen bonds between two polar molecules
-van der waals interactions : very reversible , very week
- less distance .. more overlab .. more repulsion .. more attraction
- not really interactions
- they get close to each other because they “ hate “ water
- polarity of water comes from it’s “ bent “ geometry

LEC 2 :
Slide no. Notes
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7
- Acid have conjugate base
- base have conjugate acid
- amphoteric : بذبذم
اهعم لعافتي يتلا ةداملا بسح ..
ضمحك وا ةدعاقك كلسي نا نكمم , ءاملا لثم ةبذبذم تلاعافت
9 - acid/base strength : the ability to dissociate into ions
* acid dissociate into H+
*base dissociate into OH-
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- strong acids or bases …. Straight arrow
- weak acids or bases … double arrows
- Ka > 1 : more products than reactanst … acid is stong
- Ka < 1 : less products than reactants… acid is weak
“ Remember that “
* n = m / Mm ( moles = mass / molar mass ) ….
* n = no./Av
((( Solution )))
M = mol / Mw or M = grams/(Mw * vol ) = 6.5 g / (98 * 0.2 ) = 0.33
N = M * n = 0.33 * 2 = 0.66 or another way to do it : one Eq = Mw/ions = 98/2=49
Eq in 6.5 g = 6.5/ 49 = 0.13
N = Eq / vol = 0.13 / 0.2 = 0.66 N
19 ((( soltuion )))
1 Eq of Ca ion = 40.1 / 2 = 20.1 so grams = (20.1 / 1 Eq ) * 5 * 10^- 3 Eq in blood = 100.5 gram of Ca ion in blood
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-idea of titration : you have an acid … you know the volume of it .. but you don’t know the conncentration ! so .. u add a base , till you reach neutral .. and you know the volume and conncentration of base you have added so you can calculate the conncentration of the acid !
((( Solutiion )))
(25)(0.5)=(50)(c) c = 0.25
****** BE CAREFULL ******** the doctor changed this whole slide into :
M acid * V acid * number of charges of acid = M base * V base * number of chareges of base
Can we have a minus PH ?! the doctor answer “ yes why not “
- the relation between acid strenght and Pka is reversable , but between base strength and Pka is ةيدرط
- it’s easier to take protons from H3PO4 than H2PO4 or HPO4
* PH , is an indictaor for conncentration of protons
* Pka , is an indicator for equilibirum constant
[A-] ..>> conjugate base
[HA] ..>> acid

LEC 3 :.
Slide no. Notes
1
Buffers
3
Buffer : weak acid or weak base that able to dissociate but not completely , it maintains a constant PH . ( so it is a solution that resist change in PH )
When titration CH3COOH with a base ,, firstly an immediate increase in PH will occur then when reaching a Buffering Region, this increase will be slight until the
5 end of this region and then the immediate increase returns ,, and this is the importance of a buffer .
Why ? because of the equilibrium between CH3COOH and it’s conjugate base
Buffering capacity = buffering region boundaries of it = ( pka +1 , pka-1 ) the best point where the buffer can resist the change in PH is : the point near to the midpoint .
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Boundaries of buffering region in [A-]/[HA] = 1/10 , 10/1 … How ?
PH = pka + log[A-]/[HA]
4 = 5 + log[A-]/[HA]
[A-]/[HA] = 1/10 >> from where ( pka-1 )
… and so on
Acetic acid .. their conjugate base > acetate
How do we choose a buffer ?? for example : we need PH = 4 .. we choose formate acid because 4 is nearest to it’s midpoint ( pka )
We may be asked 3 Q’s : 1- PH 2- pka 3- ratio ([A-]/[HA] )
Polyprotic : more than one proton
Carbonic acid-bicarbonate > main buffer in our blood
Proteins > able to absorb or release water in our blood
We need these buffers to maintain our blood PH = 7.4 according to survive
PH may goes as down as 7.35 & as high as 7.45
In our blood there is no H2CO3 ,, so to calculate PH we deal with CO2 rather than it BUT CO2 is a gas so we use Pressure ( Torr-mmHg )
Acidosis & Alkalosis are Pathological conditions .
CO2  >> H+  >>PH  … so kidneys reabsorb H2CO3 to balance the PH
CO2  >> H+  >> PH  ... so kidneys release H2CO3 to compensate for the lost of
H+
H+  >>CO2  >>PH  … so lungs control that by hyperventilation
H+  >>CO2  >> PH  … so lungs control that by hypoventilation

LEC 4 :
Page #2 : the slide below :
*polymers : large molecules made of monomers.
(Poly = many; mer= part) (mono = one)
* lipids are not considered as polymers, why?
Because they have different arrangements of molecules. (no obvious repeating pattern)
Page #3: the slide below:
* Dehydration reaction ( condensation reaction):

It is the reaction in which the monomers are linked together by removal of water molecule for each 2 monomers in order to build up a polymer.
*It needs energy
* Hydrolosis ( the reverse reaction ):
It is the breakdown of polymers to their monomers by addition of water.
* produce energy
Page #6 : the slide above
* monosaccharides : the simplest carbohydrates.
*disaccharides: contain 2 monosaccharides.
*oligosaccharides: contain 3 to 10 monosaccharides
*polysaccharides : contain more than 10 monosaccharides.
( "saccharo" is greek for " sugar" )
Page #7 : the slide below :
*we have to memorize the structures of :
( glucose, fructose, galactose, ribose and mannose )
*whenever you see "ose" at the end of the word, it means that this word indicates a
"suger".
*there are 2 ways 2 classify monosaccharides:
1- according to the carbonyl group they contain ( if aldehyde we call them "aldoses", if ketone we call them "ketoses")
2- according to the number of carbon atoms they contain.
( the smallest number they could have is 3 , and we call them "trioses", if 4 we call them
"tetroses" , 5 "pentoses"….. and so on ).
Page # 11: the slide above:
*chiral carbon : the carbon atom that is attached to 4 different groups.
Page # 12 : the slid e below
*example 1 : they are identical ( not stereoisomers)

*example 2 ,3 : the are stereoisomers ( not superimposable)
Page # 13 : the slide above:
What is the difference between stereoisomers and structural isomers?
*structural ( constitutional) isomers : have the same molecular formula, but a different attachments of atoms.
(They have same number of each type of atoms but the atoms are connected in a different order in them.)
*stereoisomers : have the same molecular formula . also, they have their atoms connected in same sequence( same constitution), but they differ in the arrangement of atoms in space.
Page # 13 ( the slide below):
*enantiomers : they are mirror images of each other .( not superimpoasable)
*the prefix "D-" indicates the right position of the –OH group in relation to the chiaral carbon that is the farthest from the carbonyl group.
* the prefix "L-" indicates the left position of the –OH group in relation to the
Chiral Carbon atom that is the farthest from the carbonyl group.
** "D-" means "detoxyrotatory"
** "L-" means "levorotatory"
Page # 15 ( the slide above) :
The number of possible stereoisomers of glucose is : 2^4= 16 (where the "4" number indicates the number of chiral carbons).
Page # 15 ( the slide below):
*there is a mistake in the 4th stereoisomer ( the second line to the right )
It must be like this
Page # 16 ( the slide above):
*epimers : stereoisomers that differ in orientation ( configuration) only at one carbon.
*D-Mannose & D-glucose are epimers since they differ in configuration only at C-2.
*D-Glucose & D-Galactose are epimers since they differ in configuration only at C-4.
* D-Mannose & D-Galactose are not epimers .
They are diastereoismers.
*Diastereoisomers : they are not mirror images of each other.

LEC 5 :
Slide
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*isomers: molecule that has the same molecular formula & it's divide into :
-constitutional : groups connect in different way.
-sterioisomers : they r oriented in different way .
**sterioisomers divide into :
enantiomers : mirror images and nonsuperimpossible.
-diasteriomers : not mirror images..
If there is 2 enantiomers superimpossible they r the same !
If we have glucose in the chain form so there is 10% chair & 90% ring cuz it's more stable.
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Epimers : 2 molecule that r steri. & diaste. but the group that attach 2 chiral carbon has different orientation
*glucose & mannose r diaste. & epimers.
Hemiacetal = OH + OR + H + R
Hemiketal = OH + OR + R + R
When we remove OH from hemiacetal with OR we have acetal .
Sugar that differ in the cyclic form when the hydroxyl group of c#1 is pointing downward or upward and the hydro. the only group that can rotate .
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ديعب اهدنع يش لك ليسكورديهلا امأ رفانت مهنيب ريصيو ضعب ىلع وبرقي حر هنلإ ؟ وكرحتب ام شيل يقابلاو بيط
The anomeric c in fructose is #2 .
When the hydroxyl group is omitting downward its alpha.
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تحت يملاب شيعتب يلي ةكمسلا هبشتب هنا اوركذت
When it's upward it's beta .
قوفل علاط تيب ينعي اتيب
*we don't have L- glucopyranose.
When OH in ficher in left it's up in cyclic structure & visa verse .
In Haworth projection it's an angles not vertical or horizontally & u can see it in 3-D .
Esterfication : adding of ester group.
It's important 4 phosphate 2 produce energy.
Oxidation : rxn where acid forming sugar acid so we must have OH group.
**types of it depend on which c is oxidize
Oxidation : forming acid
Reduction : forming alcohol.
Changing aldehyde group into alcohol forming hydroxyl .
N-glycosides : removing alcohol group & replacing with amino group .
**it's important in the formation of ATP
*rxn in c#2 rather than anomeric carbon .
4 the last sentences.
rxn with another c (it's the next
*rxn in amino group with c#2 so we have the formation of glucosamine.
**in the first compound ::
It's important in the forming of cartilage & ligament.
**in the second one ::
The acetate CH3COOH but acetyl CH3CO which attach to any another group & here it's attach to amino group.

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*rxn between the sugar molecule & alcohol .
*important in :
1-formation dissaca. cuz 2 monosaccar. with each other forming it & one alcohol forming glycosidic bond.
2-connect 3 sugar molecule .
When the anomeric c react with anything the ring became block ---> more stable .
*When we have the same monosacc. we call it home .... any differ we call it hetro.
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*residue : polymer residue
نيكوتل
مهيمسنب
ضعب عم اوطبتري امل امأ مهلاحل اونوكي امل لوده سب building block / subunits / precursor انع يف لأه
*the formation of it required energy & enzyme .
*disaccharides. is stable ( remember what we say about stabling anomeric carbon).
*when the molecule is stable so it need high energy 2 break it ,,, ( we break glycosidic bond 2 form monosacc.
Point 2 : he mean which carbon is involved in linkage formation the glycosidic bond

LEC 6 :
In N-glycosid the amino group is attached to anomeric carbon ( exp. Carbon num 1 in glucose )
In amino sugars the amino group is attached to somewhere else
Glycosidic bond is bond between anomeric carbon and something else
To know the difference between Galactose & glucose we look to carbon num 4 ( epimeric carbon )
Difference between reducing & non-reducing sugars that reducing sugars have free anomeric carbon
So all monosaccharides are reducing sugars .
In disaccharides , look to anomaric carbons that involve in linkage( example
: in lactose , the first sugar`s anomeric carbon involves in linkage , but the anomeric carbon in second sugar is free so lactose is reducing sugar , and maltose too )
But in sucrose, both of anomeric carbons of both sugars (glucopyronse & fructofuranose )are involve in linkage ( they are occupied ) , so sucrose is non-reducing sugar.
If u look to anomaric carbon in fructofuranose in suacrose sugar , the OH
GROUP is direct downward so u think it`s α . NO NO IT`S β , because we have flipped the fructofuranose , if u look to free fructofuranose the OH
GROUP in carbon num 3 , u will find it directs upward , but if u look to this group in fructofuronse in sacrose u will find this group directs downward , so u will realize this flipping & rotating ) ,
And that is same to CH2OH ( CARBON NUM 6)
Plz return to slide ( raffinose )
Raffinose is oligosaccharide composed of 3 monosaccharides and there are different linkages , it`s responsible for bile pain when we eat ( humus & bean )because we can`t digest it , so bacteria do that , when it`s digested ,

part of chemical reaction produces gases , so we feel stomach pain sometimes
The differences between glycogen and amylopectin are :
1-amylopectin is less branch
2-glycogen presents in animals while amylopectin presents in plants.
We can`t digest cellulose , so it`s good thing, WHY ?because it does ball
, becaust it`s bulky , then the body absorb water
) ةيدودلا ةكرحلا movement ( and ball movement become easier .
Why are fibers good ? it reduce cancer because it rid poison material from body .
The linkage (β(1_4)) in cellulose makes it straight which is fit it`s purpose ( structural polysaccharide), it`s not flexible like starch & glycogen .
The monosaccharide of pectin is D-Galacturonate , it`s oxidized in carbon num 6 , linkage is α (1_4) , some of galacturonate has ester group , so it`s heteropolysaccharide , please refer to the book .
Chitin is compoed of amino sugars ( N-Acetyl-β-D-glucosamine ) , linkage is β(1_4) .
Very important note , the linkage can`t be called β,α ( example in sucrose we can`t called the linkage α,β-(1_2)) , we just look to anomeric carbon of first sugar in disaccharides and the linkage depends on it )
The linkages in glycoaminoglycans :
1-chondritin 6-sulfate is β(1_3)
2-keratin sulfate is β(1_4)
3-heparin is β(1_4)
4-dermatan is β(1_3)
5-hyaluronate is β(1_3)
LEC 7 :

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- what are lipids ? hydrophobic macromolecules
“””not polymers “””
- have different classes ,, all of them are chains except steroids are rigns
- lipids give 9 kcal per gram , more than 4 kcal per gram given by carbohydrates .. and the metabolism must be done in the presence of oxygen (aerobic ) … ( carbohydrates can do metabolic reaction in presence of oxygen or not )
- hormones , like estrogen
- vitamins like vitamin A , D …
-shock absorber : protect internal organs
- fatty acids are simple class of lipids
- consist of hydrogen chain
- differ in length … and in our systems , the length mainly is between 14 – 24.. and the most abundant is
16 and 18
- unsaturation : presence of double bonds
Amphipathic : consist of two parts , one hydrophobic and the other is hydrophilic
- micelles : circular / hydrophilic towards the outside and the hydrophobic towards the inside
ما ظنلا نا ثيح ..
ةقاط لقا نمضي ...
ميظنتلا اذهو لكشلا اذهو بيترتلا اذه نا هانعم امب ..
انه ماع لكشب ةظحلام روتكدلا ركذو
) اربل كيليفروديهل او اوجل نوكي كبوفوردياهلا ونا ميمصتلاب دوصقملا ( ةقاط لقا ىلا اهيف جاتحي ةقيرطب ممصم ةيحلا تانئاكلاب صاخلا
- saturated … no double bonds
- monosaturated ; one double bond
-polysaturated : 2 or more double bonds
- trans is more stable BUT in our systems we have Cis
- fatty acids don’t exist as acids but as conjugate bases ?! ((( the doctor said he will ask us about this in the exam ! ))) because PH is higher than pKa … and this leads to loss of protons
- doco : 22
The ( : ) represent the number of double bonds .. but not where they are
If there is more than one double bond…and they are all cis except one is trans .. we only mention the one which is trans
مصب
@_@ it’s just a peace of cake
Omega … indicate the presence of double bonds but only the first one and we DON’t number from the carboxylic end … we number from the other side
- essential means that these molecules are important for our health and our systems but our body can’t synthesis them … and we get them from food
- linoleic is the precursor اجا نيو نم وا يشلا لصا ينعي ..
فلس اهانعم ةملكلاه of arachidonate and arachidonate give us cytokineses , and they are collectivly called “ eicosanoids “
Just memorize the names
** the doctor said u have to read the function from the book **
Aspirin stop arachidonate from converiting to prosaglandin .. and this reduce heart attacks but we have to give the paitent only a few aspirin .. because a lot of aspirin we lead to bleeding

LEC 8 : we start here from ( eicosanoids ) slide so it's #1 but 1,2,3 are in the notes before this & the doctor just repeated it quickly in the next lecture ,,, so refer to it please ^^"
Notes
PUFAs --> poly unsaturated acid .
*it's action is direct (reducing conversion....) & indirect (promoting synthesis ..... )
**more details about point 4 :: produce brain level of cholesterol & the triglycerides in our blood & that also why it's reduce the rate of heart attack.
**2 mechanism for reduce the rate of heart attack :
1-reduce the level of cholesterol in our blood.
2-prevent converting arachidonic acid into eicosanoids.
Omega-6 it's good cuz it's produce cytokines identify the disease but not all.
Oleic acid : mono nonsaturated fatty acid .
**remember it's reducing cholesterol level in the circulation so it's good.
**More # of double bond---> less melting point
*in our body double bond is cis & kink in the fatty acid .
So in the plasma membrane cuz we have this cis - double bonded fatty acid the membrane is fluidity so we have no moving ,, & cuz we have space in the bilayer membrane , molecule can move freely in the plasma membrane .
**saturated fatty acid is packed cuz ::
1-they r hydrophobic.
2-the have van dare wall interaction.
*The longer chain --> the higher melting point cuz we now have more hydrophobic with more hydrocarbons you add to the chain.
**difference between double bond & chain length ::
1-more carbon higher melting point but more double bond low melting point.
2-the double bond has larger effect than the length of hydrocarbon chain .
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Slide
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If we have cis-fatty acid --> there is kink & if we take it & add hydrogen to it --> (hydrogenation
) --> we convert it from unsaturated to saturated fatty acid.
**oil--> trans fatty acid .
**in industry ::
They take the cis fatty acid & convert it into trans fatty acid by incomplete hydrogenation reaction (cuz trans has longer path of life than the cis ) & cuz it's fluidic they think that they have the same effect.
Lipoproteins : protein with some fatty acid chain or lipid that attach to it.
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*another name of triglycerides is triacylglycerides ,, that mainly made of glycerol molecule.
*we call it tri cuz we have 3 attachment to fatty acid .
*the simplest sugar( glyceraldechile -not sure about the spelling-) 3 carbon & aldehyde group.
*simple triglyceride : 3 fatty acid the same .
*mixed triglyceride : the is a different.
*stearate : carbon fatty acid without double bond .
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*Waxes : formation of condensation of 2 molecule one of them is a fatty acid chain & the other 16

is log alcohol molecule.
*it's largely hydrophobic even though there is a part hydrophilic but the large hydrophobic & that's why it's solid.
*they have the same backbone of triglycerides which is glycerol molecule.
*1,2--> fatty acid chain but 3--> phosphate & that's why it's phospholipids so it's amphipathic molecule .
*u can add anything into phosphate & the simplest is phosphacidec acid ,,, phosphate because don't have proton (cuz it's pka is much smaller.
*lecithin in ice cream .
*serine is amino acid.
*add to point 4 this ::
From outside to inside .
*the phospholipids which are the main brain component in our cell membrane , they don't distribute equally between inner & outer.
*phosphatidylinositol more in the inner cuz it takes the signal from outside to the inside of cell.
*emulsification : the process of dissolving fat
*cuz the fatty acid is amphipathic , so the fatty acid chain surround the fat droplet & dissolve in a hydrophilic environment.
*cuz the phosphate group is exposed to the outside so this fat can be dissolved.
*plasmalogens : class of phospholipids but not made from glycerol it's from dihydroxyacetone which is as a keton group.
*from this precursor we can have many plasmalogens but this is the main structure , each one don't have custom group but ether group.
*this is different type of phospholipids structure .
*the different between liposome & micelle (they r look like a ball) ,,,
Micelle ---> the hydrophobic part is all inside , in another word : the core of it is hydrophobic.
BUT ,,, in liposome it's a combination of bilayer so we have a ball but have two layer of phospholipids & inside is mainly hydrophilic cuz of phosphate group.
*the fatty acid chain in the above have alkenes , amine group attach to different acid & they r different ,, so the simplest sphingolips has an (X) as (H) which known as ceramides.
لا يف نكل phosphate لا هيلع دحاو مقر phospholipids has higher priority more than alkenes .
< --رثيلاا
لا
هنلإ
يف هنا
سكعلا
اوركذت ..
1 مقر sphingolipid
نوبركلا ةرذ عم طبترت x *
*add this to (sphingomyelins) : which is component of myelin of nerve cells.
**add this to ( glycolipids ) : which are lipid with sugar molecule .
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27 we are sorry for any mistake ...
anything you find it useful please tell us to add it to this simple note ...
all best wishes from us to you all..
your colleges ^_^