the genentics summary

of 57

Genetics “First Exam”

*********************

Chapter 20 : Purine and Pyrmidine Metabolism.

****************************************** DNA is the genetic material in our body and it is polymer of nucleotides.

(every nucleotide = nitrogen base + pentose sugar + phosphate).

where : 1) Nitrogen base = purine or pyrmidine base.

-Purine = Adenine , Guanine , Xanthine , Hypoxanthine.

-Pyrimidine = Thymine , Cytosine , Uracil.

2) Pentose sugar = deoxy-ribose ( in DNA) or ribose (in RNA).

3) phosphate is (–ve) charged and if it is not present in nucleotide

it is called nucleoside.( nucleoside= nitrogen base + pentose sugar).

*** (((Naming Rule))) ***

Nucleotide Nucleoside Nitogeneous base

AMP ,ADP,ATP Adenosine Adenine

GMP, GDP , GTP Guanosine Guanine

XMP , XDP , XTP Xanthosine Xanthine

IMP , IDP , ITP Inosine Hypoxanthine

DTMP , DTDP , DTTP Deoxy-thymidine Thymine

CMP , CDP ,CTP Cytidine Cytosine

UMP , UDP , UTP Uridine Uracil

Functions of NUCLEOTIDES:

1) Building block.

2) Metabolic function.

3) Signaling in biochemical pathways.

4) Drugs : antibiotic , antivirals ,antineoplastics ,stimulant.

**************************************************

Properties of N-bases :

1) Planar 2) Heterocyclic 3) Aromatic 4) Nucleophilic.

************************************************

Before we start : what do we mean by metabolism??

-Metabolism : is the synthesis and breakdown of material.

but the synthesis may be either : 1) de novo or 2) salvage.

so what’s the difference between (de novo) and salvage ???

of 57

-De novo synthesis from scratch(zero).

.ا أ صغ اج١س٠ اج١ش١ذ٠ اد أ١خ عض٠ئبد صغ١شح اصفش

Salvage synthesis from existing N-base (mean recycling).

*******************************************************

In this Summary I will talk about 2 general concepts :

1) Purine metabolism : synthesis (de novo/salvage) and degradation.

2) Pyrimidine metabolism: synthesis (de novo/salvage) and degradation.

********************************************************

Now let’s start with “Purine synthesis“:

**************************************

Liver.First of all : the site of this process is in the

if we want to learn how the synthesis is occurred

we should know the structure of purine…so what’s the structure?

purine bases are 2 rings :

5 membered-ring and 6 membered-ring.

we will synthysize 5 membered-ring first then 6 membered-ring.

***************************************************

The Process of Synthesis:

***************************

(فمظ ا سؤش١ش ػ١/ال ٠ أسبء ااد ازفبػخ ابرغخ وب )

ب ابدح األ١خ ف ز اؼ١خ ؟؟... ف و ػ١خ رص١غ ٠عذ بدح أ١خ :أولا

PRPP = phosopho riposyl-5-pyrophosphate.

ى و١ف ٠ز رؾض١شب ؟

ribose 5-phosphateا شوت اي 2pثبضبفخ غػز١ فسفبد ٠ز

. pرؼط غػخ فسفبد ATPؽ١ش و ) TP2 A ) :ره ثبسزخذا

PRPP synthetaseزا ٠ز ثزؾف١ض اض٠ ٠س ٠PRPPزظ اي

and we use Mg+2

as cofactor.

********************************************

IMPخطاد رز ثشوت 01ز ابدح األ١خ سزذخ سسخ رفبػ ىخ : ثبويبا

GMP & AMPؽ١ش زا اشوت ٠زفشع غذدا ثسسز رفبػ ا

(AMP Adenine ) & ( GMP Guanine) where :

(.ثبء اماػذ ازشع١١خ) ١ ف ز اؼ١خ ازا ب ش٠ذ اصي

*********************************************

:ثذا٠خ لج ازفبص١ ٠غت ؼشفخ ؼبد ػبخ ػ ازفبػ

# The process needs 4 ATP in these 10 steps (step 2+4+5+7).

# The origin of purine atoms is :

1)Amino acids (glycin – glutamine – aspartate)

of 57

Gives Nitrogen & Carbon (#4 , #5).

2) Formate (N10

-Formyl-THF) gives Carbon #2, #8.

3) CO2 gives Carbon #6 & Oxygen

# Number of nitrogen in 2 rings = 4 so we use:

2 Gln (N9/N3)+ 1 Asp (N1) + 1 Gly (N7)

# The First step is the Committed step and first Regulated step.

# The 5 membered ring is made First before 6 membered ring.

# The phosphate group is carried through all steps this ensures that all

of intermediates and IMP remain trapped inside the cell.

# IMP is the end product of De Novo synthesis of purine.

****************************************************

Now let’s start in details :

there are 10 STEPS to convert (PRPP IMP) as it is clear in 1st table

and I will mention to control of the enzymes that catalyses some

steps in the process in the 2nd

table :

NOTES REACTION STEP & enzyme 2 phosphate group is

replaced by amine

group from

glutamine

Addition of glutamine

(Amination of PRPP).

STEP 1

Enzyme :

Glutamine PRPP

Amidotranferase.

(very important).

give 2 carbon +

1 nitrogen

(uses ATP)

Addition of Glycin.

STEP 2

Enzyme :

Transformylase.

Addition of carbon by

N10

-Formyl-THF

STEP 3

(uses ATP)

Addition of amine(N#3)

by Glutamine.

STEP 4

(uses ATP) Closure of

5 membered ring.

STEP 5

(No Biotin is needed). Carboxylation by

addition of CO2.

STEP 6

(uses ATP). Addition of Aspartate. STEP 7

Aspartate =

(amine + fumarate)

Fumarate is removed

remain amine.

STEP 8

Enzyme :

Transformylase

Addition of carbon by

N10

-Formyl-THF

STEP 9

Closure of 6

membered-ring.

Dehydration reaction STEP 10

of 57

Control of enzymes:

*******************

INHIBITED BY ACTIVITED BY ENZYME

ADP Pi PRPP synthetase

IMP + GMP + AMP PRPP

Glutamine Prpp

amidotransferase

Now the end product is IMP which convert to GMP as follow :

NOTES ENZYME REACTION Reduce NAD

+ to NADH IMP dehydrogenase IMP XMP

Addition of Glutamine

convert to glutamate

uses ATP

GMP synthetase XMP GMP

Important note : we use ATP in GMP synthesis.

Or IMP convert to AMP as follow :

NOTES ENZYME REACTION Uses GTP

add Aspartate to IMP

Adenylsuccinate

synthase

IMP adenylsuccinate

Removes fumarate. Adenylsuccinase Adenylsuccinate AMP

Important note : we use GTP in AMP synthesis.

#The accumulation of excess ATP leads to more synthesis of GMP

and excess GTP leads to more synthesis of AMP.

*****************************************************

“Control of enzymes”

******************

******************************************************

INHIBITED BY ENZYME GMP IMP dehydrogenase

AMP Adenylsuccinate synthase

of 57

Purine Nucleotide Cycle :

*****************************

This cycle takes place in muscle cells and is important…why?

because muscle cells under stress need more energy and if

carbohydrate metabolism doesn’t provide enough energy so we use

this cycle as An addition way to provide energy to cell …..but how ??

During conversion of Aspartate to Fumarate.

this fumarate is substrate in citric acid cycle so if there is more fumarate

there is more citric acid cycle(TCA) more NADH More ATP.

Now What’s this cycle ?

IMP Adenyle succinate AMP IMP(again)

AMPا IMPلب ثذا٠خ ف خطاد رؾي اي

Adenyl succinateف اخطح األ ١زظ ايASPARTATE ا ٠ز اضبفخ

AMPف اخطح اضب١خ ١زظ اي fumarateص م ثبسزخشاط

ص ام١ب شح صب١خ ثبخطر١ IMPغذدا ا AMP؟ ػذ رؾي اي cycleأ٠ رى اي

ثزه و ب رىشسد ز اؾمخ وب زظ ....ف و شح Fumarateاسبثمز١ ازبط

fumarate أوضش ثبزب صاددcitric acid cycle ثبزب صاد ازبط اطبلخATP

٠ؾمك ز اذسح؟؟ IMPا AMPاسئاي ا ؟ ب اإلض٠ از ٠ؾي اي

AMP deaminase.

now what will happen if there is deficiency of AMP deaminase?

muscle cramping and fatigue during exercise.

*****************************************************

Purine Nucleotides Degradation:

***********************************

-Let’s remember that nucleotide = base + sugar + phosphate.

degradation mean separation these 3 components from each other and

convert base to product which could be excreted outside the body.

we said that purine is either : Adenine or Guanine as main types and

2 secondary types : Xanthine and Hypoxanthine

are present during purine catabolism.

so when we talk about purine nucleotides degradation

we should talk about 2 things :

1) Adenine nucleotide degradation.

2) Guanine nucleotide degradation.

URIC ACID.The end poduct of this degradation in 2 types is : -

***************************************************

of 57

“Adenine nucleotide degradation”

**********************************

زه سجذأ ػ١خ GMPاي AMPثشوت اي purine synthesisؾ از١ب ثبي

١جم sugarص اي phosphateسم ثخطاد ززب١خ ض٠ ف١ب اي degradation…اي

از ٠غش ػ١ رفبػ صب ( Adenin or Guanine)اشئ١س baseاي

uric acid.ثؼذب رزؾي ز اماػذ اضب٠خ ا Xanthine or Hypoxanthine)٠زظ اي)

AMP CATABOLISM :

..٠ى أ ٠زت ثطش٠م١ خالي ػ١خ اذ AMPثذا٠خ اي

INOSINE اشؽخ األ اضب١خ فمظ ٠شزشوب ثشوت اي ٠خزف ز٠ اطش٠م١ ف

... ٠URIC ACIDز١ب ثشوت

: degradation of purine خالي ػ١خ اي AMPاطش٠ك األي

NOTES ENZYME REACTION

Remove phosphate &

remain (sugar+base)

Nucleotidase AMP ADENOSINE

Remove NH4+

&

remain (sugar+base)

ADA

(adenisone deaminase)

ADENOSINE

INOSINE

Remove sugar (ribose) it must be pohophorylated

before it removes.

Purine nucleoside

phosphorylase.

Inosine hypoxanthine

------------ Xanthine oxidase Hypoxanthine

xanthine

------------ Xanthine oxidase Xanthine Uric acid

Degradation of purine: خالي ػ١خ اي AMPاطش٠ك اضب


Remove NH4+

AMP deaminase AMP IMP Remove phosphate &

remain (sugar+base)

Nucleotidase

IMP INOSINE


before it removes.

Purine nucleoside

phosphorylase.

Inosine hypoxanthine

------------ Xanthine oxidase Hypoxanthine

xanthine


of 57

“Guanine nucleotide degradation”

***********************************

:٠زخص ف اغذي ا٢ر AMPثؼىس اي ٠GMPعذ طش٠ك اؽذ فمظ ذ ف اي


Remove phosphate &

remain (sugar+base)

Nucleotidase GMP GUANOSINE


before it removes.

Purine nucleoside

phosphorylase.

GUANOSINE

GUANINE

Remove NH4+

&

remain (base)

Guanine deaminase.

guanine xanthine


“ Salvage of Purine Nucleotide “

*********************************

we said that salvage mean synthesis of nucleotides from

existing purine bases and purine nucleosides.

فبرا أسدب رص١غ .....ى سىش لبػذح زشع١١خ فسفبد nucleotideؾ ؼ ثؤ اي

nucleotide فسفبد( س٠جص)٠غت أ ض١ف ػ١ب سىش .... لبػذح زشع١١خ عدح.

ؽ١ش ٠زفبػ غ امبػذح PRPPى أ٠ ؤر ثبسىش افسفبد ؟؟ شوت اي

.(N-base)ازافك غ امبػذح ازشع١١خ nucleotideازشع١١خ ٠زظ اي

The salvage pathway is clear in the following table :

The disease that results

from deficiency of enzyme ENZYME REACTION

Not included APRT Adenine + prpp

AMP

LESCH-NYHAN

SYNDROM

HGPRT Guanine + prpp

GMP

LESCH-NYHAN

SYNDROM

HGPRT Hypoxanthin + prpp

IMP

SCID (B and T cells) ADA Adenosine Inosine

The Diseases that relate with purine metabolism :

*******************************************

1) Gout Disease :

*****************

-Definition : is accumulation of Uric acid

in the synovial fluid of joints (genetic disease).

of 57

-How ??: high level of purine degradation high level of uric acid

crystallization in the synovial fluid phagocytolosis is activated by

macrophages cell lysis & inflammation.

-Why ?? (Causes) :

1) Decrease in the activity of glucose 6-phosphatase

increase production of ribose 5-phosphate by HMP shunt

increase production of PRPP.

2) Increase in the activity of PRPP synthetase

increase production of PRPP.

3) Loss of feedback inhibition of

(glutamine PRPP amidotransferase) by IMP & AMP & GMP.

4) Decrease in the actvitiy of HGPRT poor salvage

high bases high degradation of bases high Uric acid.

-Treatment : allopurinol (inhibitor of xanthine oxidase).

NOTE : GOUT is more common in males because it’s X-linked.

*************************************************

2) Lesch - Nyhan Syndrome :

************************

-Definition : is severe damage of the joints

& malfunction of nervous system (affects the neurotransmitters)

leads to unusual behavior.

-Causes : complete deficiency of HGPRT enzyme.

*******************************************

3) SCID disease : (affect B and T cells).

results from :1) Deficiency of ADA enzyme

2) High d-ATP and S-adenosylhomocysteine

Note : Purine nucleotide phosphorylation deficiency only affect T cell.

**************************************************

“ Pyrimidine Nucleotide Synthesis “

********************************

purine ب وب ف صبػخ اي..١خ ب ف و ػ١خ رص١غ ٠عذ بدح أل

ثؼ١خ Ribose 5 phosphateاز رؤر ١PRPPخ ابدح األ

purineى االخزالف اشئ١س ث١ صبػخ اي.. Hexose monophpsphate shuntاي

N-baseرضبف اي purineاي ف صبػخ PRPPأ اي pyrimidineصبػخ اي

.prppاي فق رزى اؾمز١ اشىخ مبػذح ازشع١١خػ١ب

of 57

ص ٠ضبف أال N-baseامبػذح ازشع١١خ ؼظ رصغ pyrimidineى ف صبػخ اي

.اى لبػذح فسفبد سىش Nucleotideزشى اي PRPPػ١ب اي

ارا و١ف رصغ امبػذح ازشع١١خ ثذا٠خ؟

:٠س Nucleotideؽز ٠شى اي prppاشوت ابئ از س١ضبف ػ١

…Orotate ؟ خالي اغذي ا٢ر ى و١ف ٠زشى زا اشوت:

NOTES ENZYME REACTION -Uses 2 ATP

-the rate limiting step

the committed enzyme

-CPS 2 found in cytosol

CPS 2 (Activated by :

PRPP &ATP)

(Inhibited by : UTP)

Glutamine + CO2

Carbamoyl phosphate

The ring is still open

ATCase (Activated by : ATP)

(Inhibited by : CTP)

Carbamoyl phosphate +

aspartate

carbamoyl aspartate (CA)

Doesn’t require ATP dihydroorotase CADiHydro Orotate

(DHO) Reduction of

NAD+ to NADH

occure in mitochondria

Dihydroorotate dehydrogenase

DHO Orotate

-COOص ض٠ اي ١OMPزظ اي ٠PRPPضبف ػ١ اي Orotateا٢ ثؼذ رشى اي

:از س١زفشع الؽمب core pathwayاز ٠ؼزجش ابرظ ابئ ف اي ١UMPزظ اي


------------------- orotate phosphoribosyl-transferase

OROTATE + PRPP

OMP Removal of COO

- which

react with water to give

HCO3-

OMP Decarboxylase (Inhibited by : UMP)

OMP UMP

-Now UMP is phosphorylated to UDP and UTP (ATP: Phosphate donor).

(UDP convert to d-UDP) and (UTP convert to CTP).

-we have now 2 pyrimidine nucleotides(UTP ”uracil” & CTP ”cytosine”)

-but What is the difference between UTP & CTP?

Amine group on carbon #4mean UTP is aminated on C4 to form CTP

by enzyme called : CTP synthetase.

pyrimidine nucleotides are : UTP , CTP , d-TTP

-The 1 nucleotide is remained (d-TTP ”thymine”)…How can we have it?

First we should know that TTP is only found in the deoxy form

because it’s component of DNA.

SO we must convert (UDP d-UDP d-UMP d-TMP) as follow:

of 57

NOTES ENZYME REACTION Uses Mg

+2

intermediate carrier is: Thioredoxin or

Glutaredoxin

(must be in reduced form)

Ribonucleotide

Reductase

(activated by :

low levels of dTTP)

(inhibited by : high levels

of d-TTP& high d-ATP)

UDP d-UDP

Dephosphorylation

reaction ----------------- d-UDP d-UMP

-Methylation reaction.

-Folate is used as

cofactor.

Thymidylate synthase d-UMP d-TMP

NOTE: CAD is multifunctional enzyme consist of 3 enzymes

(CPS2 + ATCase + Dihydroorotase)

-The source of methylation and the Folate is : N5 N

10 M THF.

reductionؾ ؼ ثؤ و رفبػ ٠Reductionؼزجش رفبػ d-UDPا UDPرؾي اي

٠ ؟؟أ.. Oxidation ٠ى ؼ رفبػ ٠غت أ

Reduced ٠خزضي ٠غت أ deoxy اشى اش٠جص ؽز ٠زؾي ا

.Oxidationاز ٠ؾص ػ١خ اي Reductase ض٠اإلزا ٠ز ثاسطخ

.. Reduced formى ؽز ٠ؼ اإلض٠ عذ٠ذ ٠غت أ ٠ى ثبشى اخزضي

از ٠م ثبػبدح اخزضا ؟

NADPH is the ultimate reducing source which reduce Reductase enzyme.

*******************************************************

Are all nucleotides can be present in the deoxy form? the answer is :YES.

because DNA is composed of linked nucleotides in the deoxy form.

this table show how DNA is synthesized from all deoxy nucleotides :

ENZYME REACTION

Ribonucleotide reductase.

FIRST :

ADP d-ADP

GDP d-GDP

CDP d-CDP

UDP d-UDP

Nucleoside diphosphate kinase.

SECOND :

d-ADP d-ATP

d-GDP d-GTP

d-CDP d-CTP

Thymidylate synthase.

IN DNA :

d-UDP convert to d-UMP then

d-UMP d-TMP

d-TMP d-TTP

of 57

d-CMP d-UMP

we use enzyme :

deoxycytidylate deaminase.

It can also synthesis of d-TTP as :

d-CDP d-CMP d-UMP

d-TMP d-TTP

DNA polymerase. d-ATP+ d-GTP+ d-CTP+d-TTP= DNA

***********************************************************

“ Pyrimidine Nucleotides Degradation ”

************************************

First remember that pyrimidine BASES are

(Cytosine & Thymine in DNA) and (Cytosine & Uracil in RNA).

DNA is cut to nucleotide units (d-CMP / d-TMP).

RNA is cut to nucleotide units (CMP / UMP).

By enzyme called : Nucleases.

so when we talk about pyrimidine degradation we should talk about

Degradation in DNA & Degradation in RNA.

1) Degradation in RNA : (end product = B-alanine).

*******************************************

ثذا٠خ ا ىبر األسبس١خ nucleotideػ١ب أ فص اي purine ايوب رىب ف ذ

(sugar + base +(phosphate ثبزب بن صالس ػ١بد سئ١س١خ:

dephosphorylationاصاخ افسفبد ( 0

NH4 اصاخ األ١ ( 2+

deaminationؽز سزط١غ ثؼذ اصاخ اسىش

.remove sugarاصاخ اسىش 3)

.B-alaninاز ٠زؾي أخ١شا ا ٠baseجم اي

: أ ؽست اغذ١ ا٢ر١١( 0ص 2)أ ( 2ص 0)أ ٠م ثبؼ١خ ٠nucleotideى

NOTES REACTION

Deamination reaction :

remove NH4

CMP UMP

Dephophorylation reaction :

Remove Phosphate.

Uridine = (base + sugar)

UMP Uridine

Remove sugar (ribose)

Uracil is the pyrimidine base.

Uridine Uracil

These the end product Uracil B-alanine + NH4+ + CO2

:٠ى أ ٠م ثؼ١خ اصاخ افسفبد أال ص األ١ ؽست اغذي ا٢ر

of 57

NOTES REACTION

Dephosphorylation reaction :

Remove Phosphate.

Cytidine = (base + sugar)

CMP Cytidine

Deamination reaction :

remove NH4

Cytidine Uridine

Remove sugar (ribose)

Uracil is the pyrimidine base.

Uridine Uracil

the end product Uracil B-alanine + NH4+ CO2

2) Degradation in DNA :

(end product = B-aminoisobutyrate or B-alanin)

*******************************************

we have 2 pyrimdine nucleotides in DNA :

d-CMP & d-TMP.

Degradation of d-CMP :

d-UMPأال ازبط NH4 ؽ١ش اؼ١بد ف ٠جذأ ثبصاخ ٠CMPزشبث ربب غ ذ اي

ؽست اغذي Uracilاز ٠ضاي اسىش ١زظ اي deoxyuridineص اصاخ فسفبد ازبط

NOTES REACTION

Deamination : remove NH4 d-CMP d-UMP

Dephosphoryaltion : remove P d-UMP deoxyuridine

Remove sugar (deoxyribose) Deoxyuridine Uracil

The end product Uracil B-alanine + NH4 + CO2

وبزب deoxyuridineازبط NH4ص اصاخ deoxycytidineأ اصاخ فسفبد أال ازبط

NOTES REACTION

Dephosphoryaltion : remove P d-CMP deoxycytidine

Deamination : remove NH4+

deoxycytidine deoxyuridine

Remove sugar (deoxyribose) Deoxyuridine Uracil

The end product Uracil B-alanine + NH4 + CO2

Degradation of d-TMP :

افسفبد ثؼ فمظ ض٠ ...اجذا٠خ ف NH4 ػذ عد اصاخ d-TMPب ١٠ض ذ اي

B-aminoisobutyrate ص ٠زؾي ا thymineاسىش ؾص ػ اي

NOTES REACTION

Dephosphoryaltion : remove P d-TMP deoxythymidine

Remove sugar (deoxyribose) deoxythymidine Thymine

The end product Thymine B-aminoisobytyrate

+ NH4 + CO2

of 57

Nucleotide Coenzymes synthesis : (NAD+

& FAD+ & Coenzyme A)

******************************************************

NAD+

synthesis ban be synthesized by 4 starting materials :

Tryptophan or Nicotinamide or Nicotinic acid or Quinolinate.

we will talk only about NAD+ synthesis from Nicotinamide as follow:


Prpp gives the

(ribose 5-phosphate) to

nicotinamide.

Nicotinamide

phosphoribosyl-

transferase

Nicotinamide + PRPP

Nicotinamide

mono-nucleotide

USES ATP

NAD-

pyrophosphorylase

Nicotinamide

mono-nucleotide + AMP

Nicotinamide adenine

dinucleotide (NAD)

NADP is synthesized by phosphorylation of NAD.

NOTES : 1) NAD, NADH , NADP , NADPH are involved in

reversible oxidation-reduction reaction.

2) NAD+ synthesis requires Niacin.

3) Niacin deficiency causes disease called : Pallegra.

(Pallegra is 3 diseases = Diarrhea + Dermatitis + Dementia).

*************************************************

“FAD+ synthesis”

is simple and clear in the following table :


Phosphorylation

Uses ATP

Riboflavin kinase Riboflavin+ phosphate flavin mono nucleotide(FMN)

Uses ATP FAD-pyrophosphorylase FMN + AMP FAD

Notes:

1) Flavin nucleotide serve as coenzyme or prosthetic group in protein.

2) FAD and FMN are involved in reversible oxidation-reduction reaction.

3) Deficiency of FAD causes Dermatitis in alcoholics primarily.

********************************************************

of 57

“Coenzyme A synthesis”

*********************

We use 4 ATP to produce Coenzyme A from the starting material :

Pantothenate

.ATPجزيئبث 4 اسزخذا Cysteine اضبفخ اي Coenzyme A أ ب ١٠ض رص١غ اي

( :٠ىف ف اخطاد د ؽفظ ااد ازفبػخ اارظ)اخطاد ثبزشر١ت

1) Pantothenate is phosphorylated by ATP

2) then cysteine is added in the presence of ATP

3) then CO2 is removed.

4) then AMP is added.

5) then the product is phosphorylated by ATP.

NOTE : Coenzyme A is carrier for Acyl and Acetyl groups

Coenzyme A is oxidized in TCA cycle & Fatty acid oxidative.

*******************************************************

Vitamine B12 metabolisim:

***********************************

this vitamine is called also : Cobalamine.

the functions of this vitamine are :

1) Intrinsic factor required for absorption.

2) one-carbon transfer.

example : Methionine synthesis…. So

What is the role of B12 in methionine synthesis?

Methyl B12ثزؾف١ض بدح رس homocysteine اشوت ٠methionineصغ اي

B12.رزؾي ا homocysteine اي methionineز ابدح ػذب رؾفض رص١غ اي

B12 رار ٠زؾي غذدا ا Methyl B12١شبسن شح صب١خ ف رص١غ ايmethionine.

؟Methyl B12ى أ٠ ٠ؤر شوت اي

FH4از ٠زؾي ا Methyl FH4 شوت اي

. Methyl-H4 folateاز ٠زؾي ثذس ا Methylene FH4 ٠زؾي ا FH4ا٢

:ا٢ ضؼ األش ثمبط ثس١طخ شثطب ثبىال ف األػ

1) Homocysteine Methionine (require Methyl B12).

2) Methyl B12 B12 Methyl B12 again (require Methyl FH4).

3) Methyl FH4 FH4 methylene FH4 Methyl FH4.

(require enzyme called : methionine synthetase)

now what are the diseases that result from deficiency of B12 & folate?

Megaloblastic Anemia & CNS pathology.

of 57

ى و١ف زظ اشض ؟

:٠سبػذ ف ز٠ ازفبػ١ ٠B12غت أ ؼ أ

Methyl-h4 folate H4 folate (FH4).

Homocystein Methionine.

سززشاو ااد ازفبػخ اي B12فبرا مص اف١زب١

Methyl-h4 folate & Homocystein

.ا١ غس االسب ٠functional folate & methionineمص ازبط اي

Megaloblastic anemia ٠زظ شض اي

و١ف ٠ز ػالع ؟

Treated with both B12 and folate.

Note: Folate alone can deplete CNS B12.

*************************************

“Tetrahydrobiopterin”

**********************

this coenzyme is required for Serotonin synthesis.

“serotonin is neurotransmitter”

Tetrahydrobiopterin is involved in NO synthesis.

the most important note : it is made from GTP.

***************************************

NOTE about Purine bases:

*************************

..٠غت از١١ض ث١ اماػذ اجس١٠خ ؽست ازساد ازصخ ثبؾمز١

...ىزا ١NH2س ذ٠ ضال xanthineزصخ ثؾمز١ ى اي NH2ا االد١ ٠ه

اطش٠مخ ثؤ و ع ثبسئاي سس شوجبد افشض مذس ١ض ث١اطة ارا أ)

.((ب رساد خصصخ ثززص ف١ب لبػذح زشع١١خ ا

Has “NH2” ADENINE

Has “ Oxygen , NH2 ” GUANINE

Has “ 2 Oxygen “ XANTHINE

Has “ 1 Oxygen ” HYPOXANTHINE

***************************************************

End Of Chapter 20

of 57

Chapter 2 : DNA & RNA STRUCTURE

**************************************

1) Structure of DNA & RNA (Nucleic acids):

**************************************

Nucleic acids are strands of nucleotides linked by

Phosphodiester bond (covalent bond)

The length of these strands varies as follow :

2 or 3 or 4 nucleotides. Di or Tri or Tetra nucleotides.

Less than 50 nucleotides. Oligonucleotides

more than 50 nucleotides. Polynucleotides

Nucleotide is formed from = (Sugar + Phosphate + Nitrogen-base).

where : 1) Sugar =(deoxy-ribose in DNA) & (Ribose in RNA).

2) Nitrogen base = Purine or Pyrmidine base.

-Purine = Adenine , Guanine 2 Rings.

-Pyrimidine = Cytosine, Thymine (in DNA), Uracil (in RNA) 1 ring.

(Nitrogen base determines the identity and the sequence of DNA).

Numbering of PURINE counter clockwise for 6 membered-ring.

clockwise for 5 membered ring of purine and for 6 ring of pyrimidine.

-Each polynucleotide has 2 Ends :

5 end with free phosphate group (5-terminus).

3 end with free OH group(3-terminus).

Circular polynucleotides haven’t free ends (termini).

-Between 2 nucleotides the direction of Phosphodiester bond is (35).

but the direction of the whole polymer of DNA is (53)

(OH on C#3 of the sugar binds to phosphate on C#5 of the next sugar).

-DNA has 2 portions :

1) Hydrophilic portion = (sugar + phosphate Backbone of polymer).

2) Hydrophobic portion= (nitrogen bases sticking out of the polymer).

NOTES :

1) we call : Nitrogen base(A , T , G , C ) Nucleobase.

-Nitrogen base + deoxy-ribose sugar (by glycosidic bond) Nucleoside.

-The main Nucleosides are :

(Adenosine , Guanosine , Cytidine , Uridine , Thymidine) and there are

more than 80 nucleosides is found naturally occurring nucleic acid.

-Nucleoside + phosphate (by 3-5 phosphodiester bond) Nucleotide.

of 57

2) Nucleotide is the phosphate esters of Nucleoside where :

Sugar can be phosphorylated but the base can’t be phosphorylated.

3) more than 1 phosphate can be linked to nucleoside (only to sugar)

by Anhydride linkage (di or tri or tetra – phosphate esters).

*****************************************************

What is the difference between DNA & RNA ?

RNA DNA

Single or double. Double STRAND

A , G , C ,U A , G , C , T N-BASE

Ribose Deoxy-ribose SUGAR

(A+U) and (G+C)

are not equal

(A+T) and (G+C)

are equal

Molar Rations of

Bases

Less stable More stable STABILITY

Definitions :

-Human Genome: is the whole genetic information for a certain

organism (blue-print) and it’s about 3 billion base pairs(bp) of DNA.

Human genome codes for (approx. 35,000) genes

& only 3% of human genome codes for protein.

-Genetic code : the rules that govern translation of :

(nucleotide sequence of gene amino acid sequence of protein).

************************************************

-What’s the Function of DNA ?

Preservation of genetic information from generation to generation.

this information is the genetic code that make specific protein during

process called gene expression which contain 2 main process :

1) Transcription mean convert DNA to m-RNA (in nucleus).

2) Translation mean convert m-RNA to protein (in ribosome).

**************************************************

-What’s the Shape of DNA?

in Euokaryotes(human)Linear in nucleus + Circular in mitochondria.

in Prokaryotes(bacteria , viruses , plasmids) Circular. ***************************************************

-What is the physical properties of DNA?

1) Melting point (Tm) :

-Difinition : is the Temperature when :

Half of DNA are in the random coil or single-stranded state(ssDNA).

in the other word: is the temperature at the midpoint of the transition.

of 57

-Depenedence : TM depends on :

1) The Length of DNA (longer DNA more temperature is needed)

because there are more hydrogen bonds that need to be broken.

2) G-C base Content (high G-C high TM).

so the regions that are rich with A-T have lower TM

3) Ionic strength and PH.

NOTE: There is not standered value for all DNA. It varies from one to

another because TM depends on specific nucleotide sequence of DNA.

**********************************************************

2) Denaturation of DNA separation of double strands to single strand.

-the Causes of Denaturation are:

1) Heat (more hydrogen bonds in DNA more temperature in heat)

2) High PH lead to strand separation.

**********************************************************

-What’s the Forms and Models of DNA?

1) B-DNA (Watson & crick): most common form.

2) A-DNA. 3) Z-DNA (Zigzag).

How can the scientists discover these models?

by : X-ray Diffraction studies.

-A-DNA is found under specific conditions :

Low Humidity & High Salt concentrations (or with adding alcohol).

-B-DNA is found under specific conditions :

High Humidity & Low Salt concentrations.

Z-DNA A-DNA B-DNA

left handed helix Right handed helix Right handed helix

12 nucleotides per turn 11 nucleotides per turn 10 nucleotides per turn

Longest + Thinnest Shorter + Thicker Longer + thinner -Major groove very

shallow(doesn’t exist).

-Minor groove narrower

+ very deep.

-Major groove deeper +

narrower

-Minor groove broader

+ shallower than B-DNA

Has Major & minor

grooves have the same

depth…but minor groove

is narrow.

Helical axis : in

minor groove.

Helical axis : in

major groove

Helical axis :

through base pairs.

Glycosidic bond

conformation :

Anti at C , Syn at G

Glycosidic bond

conformation :

(Anti)

Glycosidic bond

conformation :

(Anti)

--------------- Hydration: water attack

major groove.

Hydration : water attack

minor groove.

of 57

B-DNA (Watson and Crick model) : (Secondary structure)

*********************************************************

- DNA is a Double helix strands that stabilized by :

1) Hydrophobic interactions.

3) Base-Stacking interactions among aromatic bases.

2) Hydrogen bonds between N-bases:

(A-T 2 H-bonds & G-C 3 H-bonds) and must (A=T & G=C).

-the bases are stacked in the interior of the helix.

and the backbone (sugar + phosphate) located on the exterior.

-On the long of stands there are major & minor grooves between the

sugar-phosphate backbones.(major groove is much wider than minor

groove because the difference between geometry of base-pairs).

-these grooves provide a binding-site where the atoms of base-pairs can

be linked with proteins or small molecules to perform many functions

like : Compaction from DNA to Chromosome.

These double strands are Antiparallel to each other...that’s mean

one strand runs 5 3 & other strand runs 53 in the Other Direction.

*******************************************************

Notes about Z-DNA :

1) It affects the Gene expression and regulation of transcription.

2) It occurs at short sections of DNA where there are alternating

deoxyguanine (dG) & deoxycytosine(dC) on one strand and these bases

are modified by Methylation formation of Z-DNA.

**********************************************************

General Notes about DNA:

1) the Length of DNA is called : contour length.

this length varies from species to species as follow :

Plants and animals Bacteria Viruses Billions of base pairs. Millions of base pairs. Few thousands base pairs.

2) DNA is much larger than the size of cell that contains it.

so it must be packaged in the form of 46 chromosomes.

3) the length of DNA in the nucleus of human cell = 2 meter.

of 57

4) DNA is Superhelical & maybe is : Positive or Negative superhelix.

Negative Supercoiling Positive Supercoiling

Results from under-winding DNA. Results from over-winding DNA.

Occur in the nucleosome. Occur during DNA replication.

Right-handed. Left-handed.

Note: Topoisomerases (enzymes that regulate formation of superhelix).

**********************************************************

Circular DNA :

******************

-Circular DNA results from formation of phosphodiester bond

between 3 and 5 termini of linear polynucleotide by DNA Ligase.

-Some DNA molecules are sometimes linear and sometimes circular

according to their life cycle example : Phage DNA.

Important note : the strands of circular DNA cannot be irreversibly

separated by denaturation.

******************************************************

RNA : Types & Functions

**************************

-RNA is a linear polymer of ribonucleoside monophosphate.

-RNA is produced by transcription process where each RNA is

complementary to the base sequences of one strand of DNA.

-Length of RNA vary from 20 nucleotides 200.000 nucleotides.

FUNCTION TYPE

carries the Genetic Code for

specific protein which be translated

during the Genetic Expression.

mRNA

transport RNA involved in the

Translation process. t-RNA

is a part of the Ribosome

(protein Factory). r-RNA

is a part of SRP particle

which is found in ER membrane

(membrane integration).

SrpRNA

(signal recognition particle RNA)

of 57

Secondary & Tertiary structure of RNA :

Tertiary RNA Secondary RNA It is due to huge rotational

freedom in the backbone

of its non base-paired regions.

it is due to Folding

of single strand back on itself

forming Hydrogen bonding between

complementary bases on the same

strand the result is STEM LOOP.

:أشىب

1) Triplet base pairing

by hydrogen bonds.

(ex : U : A : U)

2) Base stacking.

3) Base modification.

:أشىب Stem loop types :

1) Hairpain.

2) Bulge.

3) Loop.

Base stacking mean

The bases are planar and tend to stack

by stacking forces :

Hydrophobic interaction

+ Vander Vals forces.

Stability enhance by

(base stacking in the loop)

ex : UUCG.

**************************************************

2) Compaction from DNA to Chromosome :

***************************************

DNA convert to Chromosome as follow : (important)

DNA Nucleosome Chromatin Extended Chromosome

Condensed Chromosome Chromatide Chromosome.

now the details :

1) Nucleosome = 50% DNA + 50% protein (10 nm long)

this protein is called : Histone

and it has 5 types (H1 ,H2A , H2B , H3 , H4)

Nucleosome core has a pair of each :

(H2A , H2B , H3 , H4) (8 Histones called Octamer).

٠زف ؽي ز اجشر١بد اضب١خ اشرجطخ ثجؼضب دسح وبخ DNAا٢ اي

.Nucleosomeأسثبع اذسح ١شى ب ٠ؼشف ثبي 3

CHROMATOSOMEرشى ب ٠ؼشف ثبيturns 2))دسر١ وبز١ DNAأب ارا ازف اي

so : Nucleosome = 1 ¾ turn (146 bp)

while Chromatosome = 2 turns (166 bp + H1).

Note: Chromatosome with less than 166 bp don’t bind H1.

of 57

How DNA interact with Histone to form Nucleosome?

N-terminal of histone contain positive amino acid that interact with

negative phosphate of backbone of minor groove of DNA

by Electrostatic interaction.

major groove stay unlinked and available

for interaction with proteins that regulate gene expression.

-What’s the function of H1 ?

-it is associated with linker DNA to prevent it from coiling in the place.

Notes :

1) the Histone can migrate along DNA

.Transcription and Replicationره ١سؼ إلض٠بد االصخ ؼ١بد اي

DNA. اصي ا و اي

Negative supercoilثبسز ٠ى ثبشى مرتبط DNAػذب ٠ى اي( 2

Positive supercoilثبسز ف١ى ثبشى غير مرتبط DNAأب ارا وب اي

*******************************************************

2) Chromatin = polynucleosomes linked by DNA called Linker DNA.

(between nucleosomes is 20 90 bp of linker DNA).

Notes:

1) the active form of chromatin during cell cycle is called: euchromatin.

2) the inactive form of Chromatin is called : Heterochromatin.

*****************************************************

3) Nucleofilament structure : (string of beads appearance)

Wrapping of DNA around histones to form nucleosomes results in 10-

fold reduction of the apparent length of DNA and formation of

10 nm Nucleofilament.

Now condensation of 10 nm nucleofilaments

into a solenoid arrangement( رشر١ت ج)

involving 6 or 7 chromatosomes per turn forms 30 nm fibers.

and this requires H1.

but what’s the cause of DNA compaction in the form of solenoid?

High ionic strength.

**********************************************

4) now many 30 nm nucleofilaments arrange to form Chromatide.

Chromatide is further packaging to form 2 chromatides linked by

Centromer.

of 57

Centromer : is present in each chromosome and

it’s the site for attatchment mitotic spindle during mitosis or meiosis.

******************************************************

Finally chromosome is formed by 2 chromatids linked by centromer.

Note : Packing changes during cell cycle is controlled by

covalent modification of the core Histiones (Histon remodeling).

******************************************************

3) TELOMERE :

****************

Telomere : is protective structure present at each end of chromosome.

or in other words more specific :

Telomere is the tandemly repetitive DNA

(microsatellite , repeated without interruption) at the end of chromosome.

-What’s the structure of Telomere ?

(unique DNA sequences + specialized proteins)

-What’s the Function of Telomere ?

Prevention chromosome (DNA) from shortening

(losing of genetic information) at the end of DNA replication.

-Why do we need the Telomere ?

1) Telomeres prevent the chromosome ends from being ligated together

and attacked by exonucleases (it’s enzyme that degrades DNA).

2) it attaches chromosomes to the nuclear envelope Lamina (NE lamina).

3) Telomeres begin pairing of Synapsis of homologous chromosomes

during Meiosis.

4) Telomeres can compensate for incomplete replication

of linear chromosome ends.

-How Telomere do its Function ?

-Telomerase is enzyme adds a unique sequence on the ends of

chromosomes to prevent shortening during DNA duplication.

-Telomerase enzyme binds to specific region on the parent strand and

starts copying the DNA (direction of telomere synthesis 53).

if there is no primer in DNA replication Telomerase will not work.

*******************************************************

of 57

NOTES :

1) the primer is : short strands of RNA bind to single-strand DNA

to initiate DNA synthesis.

2) Telomere is discovered in Tetrahymena macronucleus.

3) Tetrahymena cells have the sequence (TTGGGG)

while human cell have the sequence (TTAGGG).

TELOMERASE activity

In TUMOR CELL In SOMATIC CELL

The activity is very high Decrease after each cell division

They are immortal and grow

indefinitely.

chromosome shorten with each

cell divison.

********************************************************

4) Palindromes & repeated sequences :

********************************

palindromeرؼ اىخ رمشأ ا١١ وب رمشأ ا١سبس.

mean there is sequence of nucleotides in the one strand of DNA and

the same sequence of nucleotides in the other opposite strand of DNA.

mirror repeatس ازىشاس Strandارا وبذ اىز١ ػ فس اي

٠س ازىشاس strands 2ارا وبذ اىز١ ف عز١ زؼبوسز١ ػ اسسز١

palindrome.

Palindrome & mirror repeat is also called:

Symmetrical inverted repeats.

They are important because they are the sites for recognition for certain

protein that bind to DNA to perform certain function.

(EX : we can find them in the origin of replication).

*********************************************************

5) Restriction endonucleases :

*****************************

-Difinition : are the enzymes that cut DNA into small segments.

-First enzyme is found in R strain of E.coli and is called : EcoRI.

this enzyme recognizes 4-8 palindromic sequences

and cut at defined position such as (the 2nd

nucleotide).

but How can we cut ? there are 2 conditions :

1) Cutting through the double stranded DNA creating Flushed ends.

2) Cutting one strand first then 2nd

strand in the specific nucleotide

creating Staggered ends + Sticky ends.

of 57

-Benefits : cut DNA to small pieces to use it in research and diagnostic.

How can use these enzymes in the Diagnostic?

1) DNA is subjected to endonucleases obtain fragments these

fragments are separated by gel electrophoresis.

then we can know the exact sequence of the fragments.

if the sequence differ from the original sequence

we conclude that there is mutation and know the disease.

************************************************

2) we can recognize single nucleotide polymorphisms (SNP) by :

create small short fragment of DNA that we can study.

SNP mean different sequences (genotype) have the same phenotype.

EX : ATTGT ATTGT ATTGT ATTCT ATTGT…and so on.

.ث١ ش١فشاد ساص١خ ىشسح وكهىتيد واحد فقطاختالف ارا

**************************************************

3) we can also recognize single nucleotide polymorphysims (SNP) by :

Restriction fragment Length polymorphysim (RFLP)

RFLP is used to recognize SNP by knowing the sequence of short

fragment of DNA that had been cut by restriction enzyme.

then we can identify certain disease depends on RFLPs fragment.how?

ف١مطؼ ف لغ restriction endonucleasesؤر ثغ١ س١ صفخ ؼ١خ ؼشض ي

: ذ رشخ١ص ٠عذ ث شض أ ال ص ؤر ثبغ١ از ش٠...ؾذد

ؼشض وزه فس اإلض٠ فبرا ر لطؼ ف فس الغ فبغ١ س١ ال ٠عذ شض

ارا ثم اغ١ د لطغ لج اإلض٠ فبن اخزالف ف رسس اىر١ذاد ٠زؼشف

.ػ١ اإلض٠ ثبزب بن طفشح ساص١خ أشض

PCR رؼشض أال أ اشاد رشخ١ص ٠غت ى اؼ١خ غ١

.restriction enzymeلج ضغ اي

NOTES :

1) PCR = polymerase chain reaction.

2) RFLPs are useful as markers to identify particular groups of people

at risk for certain generic disorders.

********************************************************

END OF CHAPTER 2

of 57

Chapter 4 : DNA REPLICATION

****************************** -DNA Replication : is the process of producing 2 identical copies

from one original DNA molecule. (MeanDoubling of DNA).

DNA REPLICATION

TIME PLACE IMPORTANCE at S phase during cell

cycle before cell division The Nucleus at cell. Transfer genetic

information.

ؼشثثبثشى ػب زشاثظ ف اؼ١خ Replicationثذا٠خ سؤرى ػ ػ١خ اي

: ظ اؼبد ف عذاي ثبغخ االى١ض٠خ ؾفظب ؤلج اؾفظ ص س

زصز١ ثجؼضب ثشاثظ ١ذسع١١خ ث١ اماػذ strands 2ػجبسح ػ سسز١ DNAاي

ػ١ب أ فص اسسز١ ػ DNAفبرا أسدب أ م ثؼ١خ سخ اي N-BASESازشع١١خ

زا ب ٠م ث اض٠ ٠س .......ماػذثؼضب ره ثمطغ اشاثظ ا١ذسع١١خ ث١ ا

Helicase ٠فص اسسز١ ػ ثؼضب ف طمخ رس ايorigine of replication

رس .و سسخ سزى أسبسب زى٠ سسخ عذ٠ذح...فؾص ػ سسز١ فصز١

.١ب اسسخ اغذ٠ذحاز سزج ػ template strandاسسخ األص١خ ابرغخ ػ االفصبي

ؽز سزط١غ اؼ ف replication forkرس Helicaseىب االفصبي ثذا٠خ ػ اي

ال رؼدا الزفبف ؽي ثؼضب زجبػذر١ ز اطمخ ٠غت أ رجم اسسز١ فصز١

.SSB(single-strand binding protein)زا ب رم ث ثشر١بد خبصخ رس

********************************************************

:وبزب replicationا٢ ثبىبب ثذء ػ١خ اي

ا لغ ؾذد ػ RNA nucleotidesثجذء عزة اي ٠DNA primaseم اض٠ اي( 0

د سثطب ثبماػذ ازشع١١خ ثشاثظ ١ذسع١١خ ٠شى ػذد اىر١ذا templateاي

١ض١ف DNA polymerase IIIثؼذب ٠ؤر اض٠ اي RNA primerرس

ثزه ٠ى ثبء اسسخ 3اغذ٠ذح ػ ا١ذسوس١ اشرجظ ثبىشث سل Nucleotidesاي

اىر١ذ صالص افسفبد phosphate 2ره ٠سزه طبلخ رؤر رؾشس 53 ثبالرغب

اى١ر١ذ 3 اى١ر١ذ اضبف ثبىشث سل 5سل رشرجظ افسفبد ، اضبف

.Phosphodiester bond : اعد ثشاثطخ

٠ى ثبء اسسخ اب ثشى سزش أ زمطغ فبرا وب سزش س١ذ اسسخ اغذ٠ذح ( 2

leading strand ارا وب زمطغ س١ذ اسسخ اغذ٠ذح lagging strand

ى ز امطغ رجم فصخ ث سززص ثجؼضب Okazaki fragmentsطغ س١ذ ام

از رىذ RNA primer رجم وزه اي DNA Ligase ايض٠ ف١ب ثؼذ ػ طش٠ك ا

.DNA polymerase Iػ طش٠ك اض٠ ٠س ٠DNAخ ث سزسزجذي ثى١ر١ذادف اجذا

***********************************************************

of 57

now I will arrange the information in tables :

DNA replication Requires the following things DNA is douple strands and each strand

serve as a template for other strand. Template:

a piece of oligo-nucleotide of RNA

(8-10 nucleotides) that has unlinked

3' OH group in order to use it

and make 3'-5' phosphodiester bond

with new nucleotides.

Primer :

(single strand not double strand)

d-NTP(d-TTP,d-GTP,d-CTP,d-ATP) Precursors or substrates Helicase , Primase, SSB proteins ,

DNA polymerases , Ligases ,

Nucleases , Sliding clamps,

Topoisomeases.

Enzymes:

***********************************************************

Process of replication in general -Recognize the starting point.

-Separate double strands of DNA

-Primer synthesis

Initiation

-Add dNTPs to the existing strand

form phosphodiester bonds.

-Extending the DNA strand.

-Correct the mismatch bases.

Elongation

-Stop the replication.

-All the primers are removed,

-All the fragments are connected

by DNA POL I and Ligase.

Termination

***********************************************************

Features of DNA Replication

Each strand serve as template

New double-strands are

½ parent template + ½ new DNA.

-parental strands aren’t degraded.

Semi-Conservative:

-Start at both direction 3’ & 5’

-There are 2 replication forks. Bidirectional :

-One strand is synthesized

Continuously (Leading strand) +

-Other strand is synthesized

Discontinuously (Lagging strand).

Semi-Discontinuous:

-Errors must be repaird

by proofreading system.

every one billion bp only one error occurs

High Fidelty

(Accuracy) :

of 57

The Difference between leading and laggind strands :

Lagging strand Leading strand

Discontinuous (retrograde).

(Okazaki fragments = 130-200 bp)

(Okazaki in E.coli =1300-2000 bp)

Continuous (anterograde).

Form away replication fork. Form toward replication fork.

Require many primers. Require One primer

***********************************************************

DNA replication in prokaryotes (in E.coli)

Initiation :

(one origin of replication

called oriC sequence)

1-dnaA protein bind to

OriC sequence.

2- dnaB Helicase + dnaC

bind to single strand DNA

Unwind double helix.

3-SSB protein prevent reannealing.

4- dnaG bind to primase

synthesis RNA primer.

(Primosome = dnaA+dnaB+dnaG).

Elongation :

(adding nucleotides)

1-DNA polymerase III adds

d-NTPs to 3’end of the primer.

2- Form leading strand (continuous)

and lagging strand (discontinuous).

Termiantion :

(stop the replication)

1- RNA primer is removed by

DNA polymerase I.

2- Gaps is filled with nucleotides

by DNA polymerase I.

3-Nicks between okazaki fragments

is sealed by DNA Ligase.

4- remained supercoiling is relieved

by Topoisomrase II(DNA gyrase)

NOTES:

1) polymerases that working on leading and lagging strands at same

region and time are assembled into complex called : Replisome.

2) the Replisome =

2 templates + unwinding proteins + priming complex (primosome).

3) DNA polymerase III uses an RNA primer and catalyze chain growth

in 53 direction (it can’t add nucleotides de novo without primer).

***********************************************

of 57

Eukaryotic replication is similar to prokaryotic but differ in enzymes :

DNA replication in Eukaryotes -Helicase open the parental strands.

- RPA (same SSB in prokaryotes)

bind to exposed single strands.

-(pol a / primase) synthesis

RNA primer (15-30 nucleotides).

Initiation :

(multiple origins of replication)

(1 per 300 kbp)

(called autonomous sequence)

-POL delta adds d-NTPs

to 3’end of the primer. Elongation :

(adding nucleotides)

1- RNA primer is removed by

(RNase H) or (FEN 1). 2- Gaps is filled with nucleotides

by DNA polymerase delta.

Termiantion : (stop the replication)

NOTES: 1) Eukaryotic origins are shorter than prokaryotic origins.

2) Multiple origins form replication bubbles fuse together at the

end of replication give 2 daughter DNA strands.

3) If RNA primer is syntehsised on left side of bubble it will start as

lagging strand then when reach the right side it will continue as

leading strand and vise versa mean : -Each strand of the DNA has both leading and lagging strand because

the replication is bidirectional and there is 2 forks in each OriC.

4) There are 3 types of DNA sequences within OriC :

-A/T rich region : we have this region because it has less hydrogen

Bonding so it is easy to break and form single strand DNA.

-DNA box sequence: is protein-binding site in DNA synthesis.

like : binds DNA proteins to initiate dna replication.

-GATC sequence: it is a methylation site. 5) DNA primase create RNA primer in a process called

RNA polymerization.

6) Removal of RNA primar leave a gap this gap is filled with

nucleotides by DNA polymerase and remain a nick this nick is sealed

with neighboring nick by DNA ligase sealing a nick requires :

1) Formation new phosphodiester bond between nicks.

2) Energy (ATP in eukaryotes or NAD+ in prokaryotes).

7) We can separate the double strands of DNA by heat (over 90 C)

and at physiological temperature , cells use enzymes called : Helicases.

and this require ATP.

8) One of the growing strand is oriented with its 3 end toward the fork

while other is oriented with its 5 end toward the fork.

of 57

The Enzymology of DNA Replication :

************************************

1) DNA polymerases:

*********************

-REQUIRE : 1) Template 2) Primers.

-FUNCTIONS of DNA polymerases :

1) Addition of nucleotides to 3’ end of the growing chain.

2) Proofreading (correcting the mispaired nucleotides).

by : 3’5’ exonucleases (remove mispaired nucleotide from 3 end).

or 5’3’ exonucleases (remove mispaired nucleotide from 5 end).

-If an error is happened it must correct it before add new nucleotide.

Types of DNA polymerases :

*****************************

-in Prokaryotes : 5 types I , II , III , IV ,V.

DNA Polymerases in Prokaryotes (5 types)

Function: Type: Gap filling + Base excision repair Pol I

Damage bypass + DNA repair Pol II

Synthesis of DNA Pol III

Damage bypass Pol IV + Pol V

Note: POL I+POL II + POL III share in :

35 exonucleases & 53 polymerization

-the Differences between DNA Pol I and Pol III :

Pol III Pol I Has only 35 exonuclease. Has 35 and 53 exonucleases.

Adds deoxyribonucleotides to 3 end Remove RNA primer from 53

Key enzyme for synthesis of DNA It also add nucleotides to Dna chain

Synthesis both leading and lagging Only works on lagging strand

Add 1000 bp/sec

(High processivity).

Add only 1020 bp/sec

(Low processivity).

NOTES:

1) POL I is = 928 amino acids = (109 kilodalton) monomer.

2) POL III has 10 different subunits & core of enzyme has 3 subunits:

Is polymerase 1-Alpha

3’-exonuclease 2-Epsilon

Unknown function 3-Theta

Is dimer forms a ring around DNA Beta

of 57

-in Eukaryotes : there are 13 types of DNA polymerases.

DNA POL TYPE FUNCTION

-Alpha (initiation)

-Epsilon , Delta (elongation)

Chromosome replication

(initiation and elongation)

Alpha , Epsilon , Delta Double-strand break repair

Delta , Epsilon Nucleotide –excision repair

Delta , Beta , Lambda Base-excision repair

Delta , Epsilon Mismatch repair

Zeta , Iota , Kappa , Rev1 Translation synthesis

Epsilon Break-excision repair

Gamma Mitochondrial DNA replication

Theta DNA repair

Mu Nonhomologous end joining

Sigma Sister chromatin cohesion

DNA POL that share same function in both E.coli and Eukaryotes :

Eukaryotic ENAYME E.coli ENZYME FUNCTION

Pol a / primase DnaG primase Priming

Pol delta Pol III Synthesis of strands

Pol delta Pol I GAP filling

Pol Beta Pol I Base excision repair

NOTES :

1) (base excision / mismatch / double strand break) are types of

damages that can be occurred during DNA replication of the eukaryotes.

2) POL alpha has 4 subunits and has not 3’-exonucleases activity.

3) Why is there Exonucleases activity in DNA replication?

-To perform Proofreading function where it removes

incorrectly matched bases protection from mutations.

4) Processivity : is a number of nucleotides added by a DNA polymerase

enzyme per association , disassociation process.

5) Sliding Clamps : are proteins bind to DNA polymerases and hold

them in contact with the growing DNA chain

increase adding nucleotides increase processivity.

6) Sliding clamps are made of protein called : PCNA.

this PCNA form a ring around DNA double helix and this ring require

clamp loading factor called Replication factor C (RFC)

of 57

7) PCNA gives DNA polymerase (delta) unlimited processivity.

8) PCNA is homologous with prokaryotic POL III.

DNA polymerases صفخ خبصخ ثبي proocessivtyارا

:رمس اإلض٠بد ا ػ١

Processive enzyme Distributive enzyme carries out many steps of reaction before

it dissociates from the substrate.

carries out single step of reaction before

it dissociates from the substrate.

Example :

POL I = 20 cycles.

POL III = 5 million bases

POL alpha = 200

Example:

-Polymerase add single nucleotide.

-Exonuclease remove single

nucleotide.

8) DNA epsilon is highly processive but doesn’t have PCNA.

9) Why DNA Pol III works faster than DNA Pol I ?

because of the difference in processivity.

10)the 2 exonucleases activities of DNA POL I

occur at 2 different active sites.

*********************************************************

2) DNA Primase :

****************** -Definition : is RNA polymerase which creates RNA primer.

-Primer are synthesized from ribonucleoside triphosphate (not deoxy).

-Types : 1) Prokaryotic : is associated with Helicases.

2) Eukaryotic : form a complex with DNA polymerase alpha.

**********************************************************

“Untwisting parental strands” :

***************************

Parental strands wrap around each other in 2 ways:

1) Twisting of one strand around the other every 10.5 bp.

2) Coiling of the double helix on its axis (writhing or supercoiling).

now if we want to untwisting the parental strand this cause supercoiled

over wounding ahead of the fork and to solve this supercoiling we

must nick it ahead of the replication fork and this lethal problem

so what’s the true solution?

ارا أسدب فص اسسز١ ػ ثؼضب فؤؽذ اسسز١ سززف ػ األخش ثشى : ثؼ أضؼ

ال ٠ىب ارب افص ارا اضطشسب ا لطغ أؽذ اسسز١ ألع رصؾ١ؼ االزفبف

ز شىخ لبرخ فب اؾ ؟فزا س١زسجت ثبصبثخ دائخ ألؽذ اسسز١ ،

(P:ؾ ػ فص اسسز١ ػم ثجؼض ثذب صؾ ش اؾ؟ )ثبؼب١خ

-Enzyme called DNA Topoisomerases

which Cut the DNA strands, unwind them and reseal the strands.

of 57

when they do that they convert the DNA from

Postive supercoiling (contain more number of bases per turn) to

Negative supercoiling (contain less number of bases per turn)

so relieve the pressure of supercoiling.

-Topoisomerases are 2 types in human and 3 in prokaryotes:

1) Topisomerase I :

In E.coli In Human

Omega protein. Nicking-closing. NAME

Remove only

negative supercoils.

Remove both positive

& negative supercoils

FUNCTION

Breaks one strand and allows the other to rotate,

relieving the pressure, then the DNA is resealed. MECHANISM

Note : Topisomerase I cuts only one strand and make only one nick.

***********************************************************

2- Topoisomerase II :

In E.coli In Human

DNA gyrase Topoisomerase II NAME Remove positive

supercoiling and introduce

negative supercoiling

(requires ATP).

Cuts both strands of DNA,

swivels them , rejoins

them and make two nicks

(requires ATP).

FUNCTION

Creates a negative supercoiling contain less

number of bases per/turn more relaxation for

DNA unwinding will be easier..HOW?

During : break back segment then reseal

break on front side form negative supercoil.

MECAHNISM

NOTES:

1) There is Type 3 of Topoisomerases in E.coli is : Topoisomerase IV.

2)Topoisomerase II require ATP but Topoisomerase I don’t.

3) there are Antibiotics inhibit (bacterial Topoisomerase II) stop DNA

synthesis kill the bacteria.

these antibiotics are : Nalidixic acid & Novobiocin.

*****************************************************

of 57

Eukaryotic replication of Telomere :

**********************************

-Telomere : is the tandemly repetitive DNA

(G & T oligonucleotide sequence) at the end of chromosome.

-the replication of telomere require:

1) Template 2) Enzyme activity.

-this enzyme is Telomerase which have RNA serves as internal template.

Now how Telomerase does replication of Telomere ?

it recognizes the G-rich single strand at the 3 terminus and elongates it

in the 53 direction by adding telomere repeats (TTAGGG)

at the end of lagging chain.(according to slides), but in past papers they

answer the both strands leading and lagging and accord to wiki it’s both).

(it extends Telomeric sequence about 100 nucleotides).

this extension is used as template for synthesis

of the complementary strand by DNA POL alpha.

Note:

-RNA of telomerase provides mobile template associated with proteins.

***************************************************

NOTES :

1) (Ter) locus + (Ter) protein signals the end of replication where :

Ter locus mean sequence of nucleotides rich in G & T.

Ter protein contra Helicase prevents unwinding.

-What’s the difference between Telomere and TER Locus ?

TER LOCUS TELOMERE

Before the beginning

of the telomere.

At the end of linear

chromosome. LOCATION

Rich in T & G

nucleotides.

Unique sequence (TTAGGG)

+ Special proteins

STRUCTURE

Signals the end of

replication.

Prevent shortening of

chromosome thus

prevent affect genes and

cause mutations.

IMPORTANCE

2) Telomere is important in both : dividing & nondividing cells.

3) Polymerases can incorporate nucleotide analogs

that are used in killing cancer cells because cancer cells can inhibit

further synthesis or lead to high level of mutation.

of 57

4) Why in DNA replication , the primer is RNA not DNA?

-There are no enzymes could synthesize DNA fragments while

there are enzymes that could synthesize RNA primers.

let us suppose it was DNA : at the beginning of the process everything

are slow and not active so a lot of errors could happen.

but in RNA is quick and even some errors are happened in the RNA

primer but the primer will be removed at last so we will minimize

errors in having primer as RNA instead of DNA.

*************************************************

VERY IMPORTANAT NOTES

******************************

1) To indicate the templates at figure we look to the direction of strands:

the strand that has direction 5 3 from the origin of replication the

opposite strand will be the template.

2) If they give you 2 chromosome with 2 shorten end

we look to the direction of the end :

-If it is in the 3 end we complete it by: 53 polymerase.

-If it is in the 5 end we complete it by : Telomerase.

3) the DNA POL I activity that can excise mismatched nucleotides is :

35 exonucleases.

the DNA POL I activity that do Nick translation during DNA repair is :

53 exonucleases.

4) SSB keep the 2 strands apart to prevent Reannealing reduce

potential secondary structures align template strands for rapid DNA

synthesis (((SSB isn’t associated with sliding clamps))).

5) the enzyme has an associated RNA that acts as a template

for DNA synthesis is : Telomerase.

6) the following components of chromosome arrange from small to large:

Base pair Nucleotide Nucleosome Solenoid

Condensed scaffold form Metaphase Chromomsome.

7) Adjacent nucleotides are joint by : 35 phosphodiester bond.

8) To indicate which DNA has lowest melting temperature we choose the

strands rich in A-T nucleotides because have 2 H-bonds instead of 3H.

9) PCNA associate with DNA POL delta.

10) Sliding clamps isn’t found in initiation of prokaryotes replication.

11) If DNA contain 0.2 mole of Adenine(A=0.2)

of 57

what are the fractions of other nucleotides in DNA ?

A pair with T so A=T T=0.2 A+T=0.4

Tha total fraction = 1 so G+C=1-0.4=0.6 G=0.3 & C=0.3

12) To cut double-stranded DNA at specific site we use :

Restriction endonucleases.

13) Restriction endonucleases cleave DNA at : phosphodiester bonds.

14) The main replicative DNA polymerase in E.coli is : DNA pol III.

15) Structural forms of DNA (B,A,Z) can change from one to another.

16) DNA is packaged in nucleosome with : Histones.

17) The Ribonucleoside form of Hypoxanthin is : Inosine.

18) purine bases link with sugar by glycosidic bond between : C1 &N9.

pyrimidine bases link with sugar by glycosidic bond between : C1&N1

19) Purin require 4 ATP to synthisis from PRPP but it requires 6 ATP

to synthesis from zero. (PRPP require 2 ATP 2+4=6).

20) palindrome has similar sequence in similar direction.

21) the source of C6 in purines is : CO2.

but the source of C6 in pyrimidines is : ASPARTIC ACID.

22) Octamers are made of all Histones except H1.

23) the function of DNA POL beta is : base-excision repair.

24) The base that deaminates to form Thymine is : 5-mythylCytosine.

25) Wave length at maximum absorption of DNA is = 260 nm.

*********************************************************

END OF CHAPTER 4

.(( أسئخ اساد)) الؽظخ ١ عذا 25آخش

*******************************************

of 57

CHAPTER 4 : “RECOMBINATION”

*******************************

-Difinition : recombination mean :

the exchange of genetic information between 2 chromosomes mean :

transportation of Genes from chromosome to another chromosome.

-Roles of recombination in biological process:

***************************************

1) During meiosis when 2 homologous chromosomes are met they

exchange their genetic information that come from father and mother

in a process called : Crossing over.

(crossing over رجبدي اغ١بد ث١ وشس١ :ازجبدي اغ١ ٠ؼ

(.ززظ صفبد عذ٠ذح رع ع١ ف األثبء meiosisخالي ػ١خ اي

so recombination generates:

genetic diversity and new gene combinations.

2) Recombination generates New Genes.

(ex : Immuno-globulin rearrangement).

3) Integration of specific DNA element or viruse.

4) It Fixes the DNA damage (like : double-strand break).

5) It has role in Gene regulation.

6) Harmful Mutations would accumulate in each chromosome.

so recombination is one of the repair mechanism for error and

correction of this mutation.

7) Errors in recombination can lead to CANCER.

***************************************************

-What’s the practical Uses of recombination ?

1) Recombination is used in making Transgenic cells and animals.

2) it is used to determine the position of genes on chromosomes

(draw the Genetic map) ..How?

during determine Recombination Frequency which mean

the distance between 2 recombining genes along the chromosome.

-now When we say the recombination frequency between genes A and B

(for example) = 1% or 2 % …etc.

we mean in that : the distance between A and B = 1 or 2 unites.

********************************************************

of 57

Notes :

1) Recombination frequency is proportional to distance between genes.

.recombinationؽزب١خ اي أ و ب وبذ اسبفخ ث١ اغ١بد أوجش صادد ا

2) 1% frequency of recombination between 2 genes is called :

Centimorgan(cM) in human 1cM = 1 million base pairs.

**********************************************************

Types of Recombination :

NON-HOMOLOGOUS HOMOLOGOUS

Transposition Site – Specific DNA element moves from

one site to another

(little sequence Similarity)

Occurs between sequences

(limited stretch

of Similarity)

involves Specific – Site.

Occurs between identical

sequences during meiosis.

1) Homologous Recombination :

*****************************

-Is the exchange of nucleotide sequences between 2 identical DNA.

-There are 3 models of homologous recombination :

-Holiday model.

-Meselson-Radding model.

-Double strand Break model.

ثبؼشث رفبص١ ػ١خ ازجبدي اغ١ سخ اف ص سؤظ اؼبد ف ثذا٠خ سؤرى

((٠غت شبذح ف١ذ٠ أ صس ف ضشس: ))عذي ؾفظ ثبالى١ض

.)األي اجبل رؾص١ ؽبص modelزشبثخ فبرا فذ اي modelsو اي (:الؽظخ

سسز١ DNAػجبسح ػ عضء اؽذ اي chromosomeاي أولا - ى

(2 strands = duplex) ػ١ب اغ١بد اساص١خ (genes) ز اغ١بد ٠ى أ رزم ،

. صب ف وشس آخش DNAاألي ا سسخ أخش ربثؼخ شوت DNAسسخ ربثؼخ

. Recombinationزا االزمبي اغ١ ب س١ اي-

**************************************************

Holiday model :

*********************

Note : 2 Homologouos chromosomes mean 2 chromosomes that have

same genes at the same order and place.

of 57

homologous chromosomes 2 ٠زمبث meiosisخالي ػ١خ اي

:وبزب homologous recombinationرؾذس ػ١خ اي

. ف فس االغ( خزف DNAو سسخ ) رمطغ اسسز١ از س١ؾذس ث١ب ازجبدي( 0

األي زم سسخ ب ثبغ ػ اسسخ األخش DNAرفص اسسز١ اي ( 2

وزه ، ل١بب األخش ثبغ ػ اسسخ األ ثشى اضب ثؼذ فصب DNAاي

(. Holiday junctionث١ اىشس١ س١ X ٠ؼ ٠ؾذس رصبت ػ شى )زجبدي

األي غ DNAثؼذ االزمبي ازجبد ث١ اسسز١ ، ٠غت اسرجبط اسسخ ابعخ اي( 3

ره ػ طش٠ك رشى١ ساثظ ..اضب DNAاسسخ األص١خ غ١ش ابعخ اي

.ف اسسز١ ١Nitrogen basesذسع١١خ ث١ اي

ثبؾشوخ ف طمخ ازجبدي ثبزب اسزشاس ازمبي اسسخ ٠Holiday junctionجذأ اي( 4

.ؼ١ ش٠ذ ػذ رلف ازجبدي اغ١األ ا اسسخ اضب١خ ثبؼىس ؽز طي

.وتحتبج إنى طبقت .Branch migration: ز اظبشح رس

. Heteroduplexرس اطمخ از ف١ب سسخ أص١خ غ سسخ بعخ ( 5

:األبو از لطؼذ ف١ب اسالس ثؤي خطح ٠ؼبد ارصبب سثطب ثاسطخ اض٠ ٠س ( 6

.DNA Ligase.

امطغ )٠ؾذس دسا سالس األسثؼخ اىخ ىشس١ ثشى ٠ى ف١ ىبب امطغ ( 7

ويشكالن وقطت وحدة متقببهيهف اسسز١ ( single-strand nicksاأل ثبشؽخ األ

Crossover pointتسمى

.recombinationابء اي Holiday junctionثبزب اشى ٠ى عبض ؼ١خ لطغ اي

ب ٠ئد ا اسزمالي و وشس ثشى Cutting Holiday junctionؽذس ( 8

.recombinationابء اي ( اؾز ػ امطؼخ اغ١١خ ازمخ)اغذ٠ذ

.Resolution: رس ز اظبشح

:٠ى ثشى١ cuttingى زا اي

Verticalلطغ ػد ( Horizontal 2لطغ أفم ( 0

5و 3عىد انىهبيبث ( one DNA) انجيىبث انمحمىنت عهى طرفي كرومىسىو واحد :الؽظخ

Flanking Genesتسمى

let’s assume that 1st chromosome has this flanking genes

(gene X and gene Y).

and the 2nd

chromosome has this flanking genes

(gene x and gene y).

at the begening of recombination the 2 chromosomes aligned as follow:

(1st chromosome : X – Y) with (2

nd chromosome : x-y).

after the cutting vertically: the order of genes become as follow:

(1st chromosome : X – y) with (2

nd chromosome : x-Y).

Note : Branch migration is about (30 bp/s).

of 57

the Differene between 2 types of cutting :

Vertical Horizontal

Uncrossed parental

strands are cut.

ص١ز١ غ١ش اسسز١ األ(

( اشبسوز١ ف ازجبدي

Crossed strands

are cut.

اسسز١ از١ رجبدذ )

(أعضاإب خالي ازجبدي

Place of CUT

-1st chr : (X-y)

-2nd

chr : (x-Y)

-1st chr : (X-Y)

-2nd

chr : (x-y) Flanking genes

The Mechanism of Homologous Recombination in E.coli :

EVENTS ENZYME STEPS

-single-strand from each

chromosome are broken

at homologous positions in each

duplex

RecBCD

1)Nicking

strands partly unwind then

the strand from first DNA invade

the opposite strand from 2nd

DNA

forming holiday junction

(2 crossed strands).

RecA +

SSB

2) Crossing over

the portion of one invaded strand

from each duplex link with the

original strand from the other

duplex by hydrogen bonds

between complementary bases

-------------

3) Linking the 2

duplex

Holiday junction moves and

creates Heteroduplex.

(Require Energy)

RuvA

+RuvB

4) Branch migration

the regions where one strand

comes from one duplex and the

other strand comes from other

duplex are called :

Heteroduplexes.

----------

5) Heteroduplex

Nicking are resealed. DNA

Ligase

6) Sealing Nicks

all four strands are held together at

one crossover point then rotation

of this structure forms a new

holiday intermediate ready to cut.

-----------

7) Rotation(bend)

of 57

Molecules are separated by a pair

of symmetrical cuts in either of

2 directions and the ends are

resealed by Ligase.

RuvC

8) Resolution(cutting)

Notes :

2) Heteroduplex may have mismatch repair (like : Adenine with Guanine

instead of Thymine) so we must replace G with T to correct this

mismatch base pair by a process called : Gene Conversion.

so Gene conversion is : converting one allel into another by replacing its

mismatched base pairs into correct one.

Allel) : عضء اغ١ ( أ١١اغ١ ٠سبAB )ؽشف اؽذ ضال = ١أ األ: (A

3)Region of Heteroduplex contains at least one mismatched base pair.

**********************************************************

Meselson-Radding Model :

****************************

the mechanism of this model is similar to holiday model but there is some

difference as follow :

1) 2 homologous DNA molecules come together aligned single strand

break is made in one strand.

2) The 3-OH end of the nicking strand is elongated by DNA polymerase

displacing the 5’ end.

3) The free 5’ end invades the other duplex forming D-loop.

4) D-loop is degraded then the invaded strand reseal with the duplex

by DNA ligase so we see : one strand crosses between 2 duplex.

5) Now branch migration occurs as one strand is elongated.

6) The elongating strand cross over and is joined to the opposite duplex

forming 4 strands joined at 1 cross over point form Holiday junction.

7) Rotation of the strands and form new holiday junction ready to cut.

8) Resolution : is occurred in 2 ways :

-cut holiday junction Horizontally: so flanking genes (XY) with (xy).

-cut holiday junction Vertically: so flanking genes (Xy) with (xY).

**********************************************************

NOTES:

1) The Heteroduplex here is not reciprocal

mean it is only found on one duplex.

2) Mismatch repair in the Heteroduplex can lead to gene conversion.

3) Holiday junction can be resolved 2 ways (horizontally and vertically)

only vertical way produce true recombinant molecule.

of 57

Double Strand Break Model :

*******************************

the mechanism of this model as follow :

1) Initiation by double strand break in one DNA(one chromosome).

2) DNA is resected(cut) from the break by an exonuclease.

3) 3’ end of the broken strand invade the other duplex.

4) Now may be occur mismatch base pair so enzymes of mismatch

repair resect the free end remove the mismatch base.

5) After removing the false base and correct the error we must put the

correct base by Gene Conversion where the free end is extended by

DNA Polymerase.

6) Remaining Nicks are repaired then forming 2 Holiday junctions.

7) Resolution : there are 2 junctions so there are to cuts 2 ways in

each cut 2*2 = 4 possible result

(horizontally/horizontally or vertically/vertically

or horizontally/vertically or vertically/horizontally)

Notes:

1) Resolution can occur by Topoisomerase type II.

2) Meiotic recombination in Yeast is initiated by double strand break.

****************************************************

now we will compare the 3 previous models and (this very important) :

Double Strand

Break model

Meselson-

Radding model

Holiday model FEATURES

Yes Yes Yes HOMOLOGY 1 double strand

break ends are

resected

1 single strand

nick

2 single strand

nicks at

homologous

positions

INITIATION

1 or 2 strands

invade other

duplex

Single elongated

nick strand

invades other

duplex

1 strand of each

duplex invades

the other.

(reciprocal)

STRAND

INVASION

Yes Yes Yes BRANCH

MIGRATION 2 Holiday

junctions

Holiday junction Holiday junction KEY

INTERMEDIATE Asymmetrical Asymmetrical Symmetrical HETERODUPLEX

*********************************************************

of 57

Examples of homologous recombination :

2-Intramolecular 1-Intermolecular 2)Inverted Repeats 1)Direct Repeats 2)Double Cross over 1)Single Cross over

Change the direct

of sequence.

Don’t change the

direct of sequence

Has 2 cuts 2

holiday junctions.

Has 1 holiday

junction.

The Key proteins of Recombination in E.coli :

*****************************************

-The key protein in recombination of E.coli is: RecA.

-There are also proteins like : RecBCD , RuvA , RuvB , RuvC

involved in recombination and has multiple activities.

RecBCD : has 3 subunits B,C,D.

FUNCTION Enzyme

35 Helicase + Nuclease RecB

Recognize Chi

(crossover hotspot instigator)

RecC

53 Helicase RecD

Note:

Chi sequence is : specific site where DNA should be cut and broken.

so RecBCD has :

1) Endonuclease subunits (RecBC) Cut one DNA strand close to Chi

sequence (Chi sequence is : GCTGGTGG, found every 5000 bp).

2) DNA Helicase activity (RecD) and DNA-dependent ATpase activity.

Unwinds DNA to generate the 3’ single strand tails (ss tails).

RecBCD pathway of Homologous Recombination : 1-Nick is created in one strand by RecBCD at Chi sequence.

2-Unwinding DNA by RecBCD binding of SSB and RecA.

3-RecA promots strand from 1st DNA to invade the 2

nd DNA

displacing 1 strand from 2nd

DNA form D-loop.

4-The displacing strand in 2nd

DNA link with

the original single strand in the 1st DNA.

5-The displaced strand and the invaded strand are nicked by RecBCD

complete strand exchange form holiday junction.

6-Nicks are sealed by DNA ligase.

7-Then branch migration by (ruvA +ruvB).

8-Resolution of Holiday junction by (ruvC).

of 57

RecA protein :

***************

-RecA binds to single-strand DNA (SS DNA) from 1st chromosome

and catalyze it to invade the other double strand DNA(2nd

chromosome).

-it is very important protein for many types of recombination

(such as :during meiosis in yeast).

-RecA polymerizes onto single strand DNA and 53.

it catalyzes strand exchange as follow :

Mechanism of strand exchange by RecA : RecA coats single stranded DNA

(accelerated by SSB

get more relaxed structure).

1) Pre-Synapsis :

mean single strand align with double

strand by complementary sequences to

form 3 stranded D-loop structure.

2) Synapsis :

single strand DNA replaces the same

strand in the duplex to form

new double strand DNA.

(Requires ATP hydrolysis).

3) Post-synapsis :

(strand exchange)

RuvA & RuvB :

****************

-RuvA & RuvB are DNA helicase that catalyzes branch migration.

-RuvA is tetramer while RuvB is hexamere ring.

and both RuvA & RuvB bind to holiday junction.

RuvA forces it into square planar conformation.

RuvB has helicase & ATpase activity.

NOTE:

1) 2 copies of RuvB bind to (RuvA and 2 DNA helicases)

at holiday junction.

2)Branch migration is in the direction of RecA mediated strand-exchange.

*********************************************************

RuvC (Resolvase):

*****************

RuvC is an endonuclease that cuts 2 strands of holiday junction.

it binds to Holiday junction as dimer (that has RuvA & RuvB).

-its main function : catalyzes the resolution of holiday junction(HJ).

of 57

Note:

1) There are 2 models for binding RuvA & RuvB & RuvC to HJ :

1) Alternate RuvAB-junction complex.

2) Putative RuvABC-junction complex.

2) Branch migration is needed to reach consensus sequence is :

(A/T)TT(G/C) which occur frequently in E.coli genome.

*******************************************************

Non-Homologous recombination :

**********************************

Site-Specific recombination :

-Site-specific recombination is used by both eukaryotes and prokaryotes

to regulate gene expression and to increase the organisms genetic range.

-Viruses and transposable elements often integrate their genomes into the

host chromosome.

**********************************************************

Repair of Double strand breaks (DSBs) in nondividng or Mitiotic cells:

********************************************************

-DSBs is the most sever form of DNA damage.

-It causes : 1) Loss of genes 2) Cell death.

-It is caused by :

1) Ionizing radiation. 2) Certain chemicals. 3) Torsional stress.

4) Some enzymes (Topoisomerase , Endonucleases).

Now how can we repair DSBs ? there are 2 general ways to repair DSBs:

Non-homologous end joining

(NHEJ)

Homologous recombination

(HR) -it is Ligating nonhomologous

ends.

-Repair of broken DNA using

intact homologue.

-Ends can be damaged before

religation (genetic material lost)

or get translocations.

Very similar to meiotic recombination

-Prone to error. -Very accurate.

NOTE : NHEJ is used more than HR in plants and animals.

*********************************************************

End of Recombiantion (lecture 6)

of 57

Chapter 4 : “Mutation and DNA Repair”

********************************* : is the change of genetic material Mutation-

mean change in the sequences of nucleotides in DNA.

mean change in genetic code so change in the result protein.

of Mutation :Causes The

1) Error during DNA replication or DNA repair.

2) DNA damage by the following factors :

1-Reactive oxygen species(ROS) from metabolism.

2-Environmental agents : Chemicals , ionizing Radiation , UV light.

3- Carcinogens and Mutagens attack DNA.

4-Unwanted spontaneous chemical reactions such as :

a) Deamination of Cytosine , Adenine , Guanine

result : Uracil ,Hypoxanthine , Xanthine respectively.

-Deamination of cytocsine is considered point mutation(transition).

b) Loss of purin Bases (200010000 n/day) by process called

Depurination generating gap this gap is called :

(Apurinic Site(AP) or abasic Site) the backbone still intact.

Notes :

1) Mutation may be harmful (cause genetic illness or cancer).

-Mutation may be beneficial (rarely).

-Mutation may have no effect on the organism for 2 reasons :

-Mutation occurs outside the gene.

-Degeneration of genetic code.

2) In Humans : there is 10 mutations every replication cycle in each cell.

3) UV light causes pyrimidine Dimers.

*******************************************************

“POINT Mutations : changes of single base-pair” :

******************************************

ىر١ذاد ززب١خ 3رس و .. Nucleotidesػجبسح ػ رسس اي DNAاي: أولا

.ؼ١ الزبط ثشر١ ؼ١ amino acidاسئخ ػ رى٠ genetic codeاش١فشح اساص١خ

أ رزغ١ش ره اش١فشح اساص١خ ثؾذس رغ١ش ػ : (mutation)١خاطفشح اساص: ثبويبا

. اسئخ ػ ٠زغ١ش اجشر١ ابرظ amino acidىر١ذارب ثبزب ٠زغ١ش اي

.اضبفخ ىر١ذ أ ؽزف ىر١ذ أ اسزجذاي ىر١ذ ثآخش: زا ازغ١ش أشىبي

:ازفبص١ ؽست اغذي ا٢ر

of 57

EXAMPLE TYPE

ACGUAU ACGUCU (A to C) single

effect : change the amino acid.

Missense

mutation

Substitution ACGUAU ACGUAA (U to A) UAA

effect : stop the synthesis of protein.

Nonsense

mutation

ACGUUAA ACGUAA

effect : change many amino acids

change whole protein (finally stop).

Frameshift Insertion

(addition)

ACGUAAUCA ACGAAUCA

effect : change many amino acids

change whole protein (finally stop).

Frameshift

Deletion

CGG(CGG)45CGGCGG(CGG)102CGG

effect: increase number of similar codon.

Can cause

Disease Triplet

expansion

-Substitution mutation has 2 types :

1) Transitions: where one purine is substituted for another purine.

Or one pyrimidine is substituted for another pyrimidine.

2) Transversions: where one purine is substituted for

another pyrimidine. and vise versa.

:طجؼب بضع وز١ش أب و١ف ثغ اسئاي ػ١ ثبالزؾب وبزب

substitution of G instead of A is called : ….ans : Transion …and so on.

which mutation in sequence GGATCA(example) represents transversion?

فشوض ػ أ اب framshift mutationازب١خ رض mutationى ٠سؤ أ اي

سسخ ٠ سػ ٠ؼطب ثبسئاي nucleotideؽزف أ اضبفخ

***********************************************************

Notes :

1) Silent or synonymous mutation : is change in the 3rd

nucleotide of

codonbut don’t change result amino acidso hasn’t harmful event.

2) The diseases that result from triplet expansion are :

Huntington disease & Fragile X disease.

3)Some chemicals : Acridines & Proflavin cause insertion or deletion.

4) Frameshift mutation causes all of the codons after it to be different.

********************************************************

DNA Repair :

***************

if DNA is damaged, it must be repaired..and there are many types of

repair system classified according to type of damage.

the damage is often occured at N-base in DNA.

of 57

-if damage happen at only single strand of DNA the repair systems are:

Difinition TYPE

When the base is damaged (abnormal

nucleotide)

and repaired without remove from the DNA.

((mean repair directly)).

1) Direct repair

When the base is damaged (abnormal

nucleotide)

and repaired by remove it from DNA and

replace it with the intact one.

2) Excision repair

Is similar to excision repair but the mutation is

base-pair mismatch (ex :A with C) not

Abnormal nucleotide.

3) Mismatch repair

When mutation cause gap in synthesis of DNA

during DNA replication.

4) Recombinatial

repair

-if damage happen at double strand of DNA the repair systems are :

1) Homologous Recombination(HR).

2) Non-Homologous End joining(NHEJ).

we talk about these types previously.

*********************************************************

now we will talk about the mechanism of all repair systems in details :

1) Direct Repair :

****************

ػ اىر١ذ اصبة ف اسسخ ص ٠ض٠ ٠DNA nucleaseزؼشف اض٠ اي: ثشى ػب

١أل زا افشاؽ ثبىر١ذ ابست ٠Dna polymeraseجم ىب فشاؽ ، ٠ؤر ثؼذ اض٠ اي

.١شثظ اىر١ذ اضبف غ اسسخ األص١خ DNA Ligase، ص ٠ؤر اض٠ اي

ENZYME STEP

DNA nuclease. 1) Finding the damge and cut it out.

DNA polymerase. 2) Fill the gap by nucleotide

according to complementary strand.

DNA Ligase. 3) Ligation parts of repaired strand.

Examples of Direct Repair:

a) Photoreactivation of pyrimidine Dimers:

-First Dimer mean 2 nucleotides are linked as 1 piece, but what’s the

cause of that? it is UV lightcause dimerization of adjacent pyrimidines.

of 57

-Most common dimerization is with Thymines.

-Now what’s the mrchanism of photoreactivation repair?

٠شرجظ ث ثعد thymine dimerػ اي ٠DNA photolyaseزؼشف اض٠ ٠س

visible light ٠م زا اإلض٠ ثؼcleavage dimer اػبدح وthymine

.dimer 2 normal nucleotides)))))). ا ضؼ اطج١ؼ د دظ

-Note: DNA photolyase isn’t found in human.

**********************************************************

b) Direct Demethylation :

DNAف اي Cytosineغ اي Guanineف اؾبخ اطج١ؼ١خ ٠شرجظ اي

٠O6-methyl guanineزظ شوت اس methylationى ارا ؽص غا١

.mutationزا طجؼب thymineزا اشوت س١شرجظ غ اي

أ أؽذ ؽا اي carcinogensا اغا١ ؟؟ methyl group از م اي

methyl ف اخ١خ ضال :S-adenosyl-Methionine.

؟ mutationارا ا٢ و١ف ٠ز اصالػ ز اي

ػ O6-methyl guanine methyl transferase(MGMT):٠زؼشف اض٠ ٠س

cytosine ٠مب ا اي ٠methylض٠ غػخ اي O6-methyl guanine اي

. degradationزا اإلض٠ ص inactivationب ٠ئد ا ..اعدح ف اإلض٠ فس

so that single molecule of MGMT can remove only one methyl group.

**********************************************************

2) Excision Repair :

******************

-Definition : it is removal of the damaged nucleotide(s) then leaving

gap in the DNA then fill this gap by resynthesis of nucleotide then

ligation to restore the continuity of the DNA.

there are 2 types of excision repair :

a) Base excision repair.

b) Nucleotide excision repair.

a) Base Excision Repair:

**********************

it repairs : Methylated bases ,, Deaminated bases (ex: Uracil that result

from deamination of Cytosine) ,, Oxidized bases ,, AP(Abasic) sites.

-The Mechanism :

٠ض٠ ثمطغ اشاثطخ damaged baseػ اي ٠DNA glycosylaseزؼشف اض٠ اي

أب اشاثطخ . nucleotideف اي sugarاي baseاعدح ث١ اي glycosidicاي

اض٠ ث١ اسىش افسفبد ال رمطغ لج زا اإلض٠ ث ٠م ثمطؼب phosphodiesterاي

اض٠ ٠س ٠3ى اصاخ اسىش ربب اب٠خ 5مه انىهبيت ٠AP endonucleaseس

of 57

AP lyase . ا٢ ثم فشاؽgap ٠ال زا افشاؽ ..ىب امبػذح اسىش از٠ ر اصازب

.ligated by DNA Ligase ص DNA polymerase I ىر١ذ عذ٠ذ ثاسطخ اض٠

NOTE: there are at least 8 different glycosylases in humans.

one of these enzymes : Uracil DNA glycosylase(UNG).

***************************************************

b) Nucleotide Excision Repair :

**************************

it repairs : pyrimidine dimer , large and chemical adducts caused by

cisplatin (cancer chemotherapy) (adducts mean piece of DNA

covalently bonded to (cancer-causing) chemical).

-The Mechanism:

:ى أ اخزالف )غ اخزالفبد ثس١طخ base excision repairفس آ١خ اي

in base excision repair we remove one base.

but in nucleotide excision repair we remove many bases or

nucleotides(27-29 nucleotides) around damaged base in human).

ENZYME STEP

UvrA + UvrB + UvrC. 1) The damaged base is recognized.

Endonuclease nicks the DNA

backbone on both sides of the

damage.

2) Segment around damaged base is

removed by enzyme that make 2

nicks in the damaged strand.

Exonuclease or Helicase removes

the damaged DNA.

3) 27-29 nucleotides is released

leaving a gap.

DNA polymerase I in bacteria.

DNA delta or epsilon in eukaryotes.

4) Resynthesis (fills the gap).

DNA ligase. 5) The remaining nick is sealed

NOTES :

1) The 3rd

type of excision repair is called :

Transcription-Coupled repair.

2) It repairs the damage that prevent DNA from doing

Transcription process.

3)The Nucleotide repair system in eukaryotes make larger gap than in

prokaryotes and (the largest gap in DNA repair system).

4) The responsible for correction of pyrimidine dimers in humans is :

Nucleotide excision repair.

**********************************************************

of 57

3) Mismatched Repair :

********************

it is used to repair : misincorporated bases during replication and missed

by the proofreading function of DNA polymerase (exonuclease).

mean it removes the replication errors.

-Important Note:

Mismatches are not like DNA Damagethere is no damaged or modified

base present just present the wrong base (like: A with G instead of T).

-The Mechanism :

أ األد١ ٠شرجظ غ اس١زص٠ ضال ثذال اضب١٠ ١س base pairلب اخطؤ ٠ى ثبي

damage ثبيbase زا ٠ؼ أ ايbases ازمبثز١ ثبسسز١ ايtemplate and

daughter strand ال ٠ى خطؤ أ الؽظ اال ثؼذ ازبء اي..س١ز١replication أ

. newly daughter strandػ اي templateف الذ از ال ٠ىب ف١ ر١١ض اي

اعد ػ baseاخطؤ ال ذس ف١ب ارا وب سض٠ اي baseأ طبب ال ٠عذ اصبثخ ر١ض اي

baseارا أخطؤ اغس أصاي اي daughter strandاعد ػ اي baseأ اي templateاي

ارا ب اؾ ؟؟؟..بد اساص١خفمذ ؼ mutationزا س١سجت templateاعدح ػ اي

DNA Methylation ..بن اض٠بد لبدسح ػ اضبفخ ١ض١ ا ايnewly strand لج

templateػ اي daughter strandثبزب ٠ىب خالي فزشح لص١شح ر١١ض اي templateاي

.ز اسسخ اخطؤ baseثؼذ ض٠ اي strand خالي الؽظخ ا١ض١ ػ أ

DNA methylation in E.coil differ from methylation in human as follow:

1) In E. coli :

-Methyl is added on the Adenine(A) within GATC sequence.

2) In human :

-Methyl is added on the cytosine(C) within CG sequence.

and in both cases : the sequence is a palindrome.

so we uses hemimethylated strand to determine

which is correct sequence

Notes:

1)Methyl-directed DNA repair pathway of E.coli is example of :

Mismatch repair system.

2) Defects in Mismatch repair cause :

Hereditary nonpolyposis colon cancer (HNPCC).

*************************************************

of 57

Recombinatial Repair :

*********************

During the replication , If template is damaged the replication is

stopped because DNA polymerases can’t add new nucleotides opposite

damaged bases and this leaves a gapthis gap is lethal to DNA if it

isn’t repaired …so how can we repair these lesions and fill the gap ?

by 2 repair systems :

1) Bypass synthesis.

2) Daughter strand gap repair.

1) Bypass synthesis :

******************

there are specialized DNA polymerases with relaxed specificity can add

nucleotides opposite lesions(damage) in the template so allow bypass

of damage and synthesis of nongapped daughter strands.

Note:

1) Relaxed specificity and lack of proofreading means

introduce the errors (mutations).

2) The mutation can be limited with low processivity

(less than 10 nucleoties).

***********************************************************

2) Daughter strand gap repair :

****************************

أ ا١٢خ وبذ ثضغ ىر١ذاد ىب افشاؽ ص اوبي bypassلب ثبؼ١خ اسبثمخ

.leadingزا اىال ٠ى فؼبي طم ارا وبذ اسسخ اغذ٠ذح .. replicationاي

س١ؾص okazaki fragmentsأ laggingا٢ برا وب اسسخ اغذ٠ذح ...أ سزشح

ب اؾ ؟؟؟ ..او ص جبششح رزم صغ لطؼخ عذ٠ذح رشن افشاؽفشاؽ ف لطؼخ أوبص

RECOMBINATION از س١أل افشاؽ ؟؟؟؟ ا اي

daughter strand gap repair is by recombination between 2 new duplexes

this allow transfer a piece of normal parental strand into the gap.

but the new gap will create in the parental strand that give the piece.

this new gap will be filled by DNA polymerase and sealed by DNA ligase

the result : the gap is repaired although the lesion remains.

now we can repair the lesion by excision repair system.

**********************************************************

of 57

Regulation of DNA repair : (SOS regulon)

**************************************

-If damage is happened to DNA it triggers the SOS resonse.

-SOS response is : change in gene expression that aids in

recovery from Damage.

but what’s the SOS regulon ??

-Regulon is a group of operons that are controlled by common repressor.

)). unit made up of linked genes((operon mean :

((repressor mean : regulator)).

-The genes which are present in SOS regulon are :

uvrA ,uvrB ,uvrC , recA , lexA.

-Now complex process causes induction of many genes that are regulated

by common repressor lexA.

**********************************************************

Possible consequences of gene mutations outside the coding sequence :

*********************************************************

if mutation is happened to DNA in known noncoding sequences

EFFECT SEQUENCE -May increase or decrease the rate of

transcription Promoter

-May disrupt the ability of gene to be

properly regulated. Response element

(operator site)

-May alter the ability of m-RNA to be

translated / may alterm-RNA stability. 5’UTR / 3’UTR

-May alter the ability of pre-mRNA

to be properly spliced. SPLIC recognition

Notes about previous table:

-Promoter mean : region of DNA initiates transcription of particular gene.

-Response element : short sequences of DNA binds to transcription

factors and regulate transcription of genes.

-UTR = UnTranslated Region.

**********************************************************

repair systemخص اإلض٠بد اعدح ثؤاع اي

of 57

ENZYMES/ PROTEINS REPAIR SYSTEM DNA Glycosylase

AP Endonuclease

DNA Polymerase I

DNA Ligase

BASE EXCISION

Uvr-A , Uvr-B , Uvr-C

DNA Polymerase I

DNA ligase

NUCLEOTIDE EXCISION

DAM methylase

MutS ,MutL ,MutH

Exonuclease

DNA Helicase

SSB protein

DNA Polymerase III

DNA Ligase

MISMATCH

NOTES about Chapter 20: (importatnt)

**********************************

1) Some Abbreviation in the summary :

APRT = Adenine Phosphoribosyl Transferase.

ADA = Adenosine DeAminase.

HGPRT= Hypoxanthine-guanine phosphoribosyl transferase.

SCID= severe combined immunodeficiency disease.

ATcase or ACTase = Aspartic Carbamoyl transferase.

2)ATcase enzyme is regulated(activation or inhibition) only in bacteria.

while CPS II enzyme is regulated in mammals.

3) CPS I is found in mitochondria while CPS II in cytosol.

4) CTP has no effect on CPS II in bacteria.

5) Orotic acid Urea disease is caused by deficiency of :

OMP decarboxylase.

6) Uracil and Thymidine are degraded by reduction by enzyme called :

Dihydropyrimidine dehydrogenase.

7) The Rate limiting step in purine synthesis is catalyzed by :

Amidotransferase.

8) ADP is a noncompetitive inhibitor of PRPP synthetas

,not competitive.

9) The similarities between purines and pyrimdines are :

-Both contain Hexagonal ring(mean 6 ring).

of 57

-Both use Glutmine and aspartic acid as a source of Nitrogen in synthesis.

-Both use amino acids and CO2 as a source of carbon atoms in synthesis.

10) When they ask about the final products of the core pathway in purine

synthesis it’s only IMP, not IMP+GMP+AMP.(I said core pathway).

9)The inhibitors of IMP dehydrogenase are: GMP + Mycophenolic acid

11) In the First committed step in purine synthesis :

when we say that glutamine PRPP amidotransferase enzyme

(the main enzyme in purine synthesis) is converted into the dimer form

we mean inhibiting this enzyme so inhibitors of this enzyme :

IMP + GMP + AMP converts it to dimer form (dimerization).

and activator is PRPP that its activation and effect is ALLOSTERIC.

but The effect of glutamine is : HYPERBOLIC.

12) Gout disease isn’t accumaltion of uric acid in joints only.

maybe occur in other places.

13) pyrimidine de nove synthesis occurs in 6 STEPS in cytosol. And

only the fourh step (formation of Orotate) occur in mitochondria.

14) Human and Bacteria can synthesis nucleotides.

15) Bases and Nucleosides can pass cell membrane

But Nucleotides cannot pass cell membrane.(important).

16)Ribonucleotides are present at millimolar concentration.

but Deoxynucleotides are present at micromolar concentration.

17) Vitamin B12 deficiency leads to convulsion and increase methyl THF

& Megaloblastic anemia & deficiency of Methionine not accumulation.

18) the Mitochondrial enzyme in pyrimidine synthesis is :

Dihydroorotate dehydrogenase.

19) PRPP is used at step number 5 in Pyrimidine synthesis.

20) the source of Methylation in thymine synthesis is :

N5 N10 Methylene THF.

21) Cytosine and Thymine are synthesized using metabolites of Uracil.

22) Methotrexate decrease the rate of Purine synthesis.

23) the committed step in pyrimidine synthesis is : the Second step.

24) Methylcytosines are common sites for mutations …. WHY????

because when it is deaminated prevent discrimination

between daughter and parental strand.

25) if the mutation eliminates the AP site

endonuclease show decreased excision repair.

**********************************************************

of 57

:recombinationء مع تصحيحهب في انمهخص انشبمم ومهخص الاألخطب

TRUE FALSE Chapter/PAGE GMP guanosine AMP guanosine Chapter 20 / page 8

RNA is cut to

nucleotide units

(cmp/ump)

RNA is cut to

nucleotide units

(dcmp/dump)

Chapter 20 / page 12

DNA has 2 portions :

1)hydrophilic(sugar).

2) hydrophobic (base).

DNA has 2 portions :

1)hydrophobic(sugar).

2) hydrophilic(base).

Chapter 2 / page 17

minor

groovebroader

Table (A-DNA)

minor groove deeper

Chapter 2/ page 19

٠DNAم اض٠ اي

primase ثجذء عزة اي....

rna primaseاض٠ اي٠م

.... ثجذء عزة اي

Chapter 4/ page 27

5’3’ exonucleases

(remove mispaired

nucleotidefrom 5 end).

5’3’ exonucleases

(remove mispaired

nucleotidefrom 3 end).

Chapter 4 / page 31

Table (thus prevent

affect genes and cause

mutations).

Table(thus affect genes

and cause mutations).

Chapter 4 / page 35

اؾشف ااؽذ = نيماأل أ

Aضال

اؾشف ااؽذ = أ اغ١

Aضال

Chapter 4

(recombination)

(2nd

summary)/ page 5

((ع ال٠خطئ ))زا اغذي لبث زؼذ٠ ارا عذ أخطبء عذ٠ذح ف اخص اؾب

.06صفؾخ 21رؤوذ أ٠ضب اضبفخ فمشح عذ٠ذح ب٠خ رشبثزش

**********************************************************

END OF THE SUMMARY

I HOPE FOR YOU ALL THE BEST ^_^

فمى هللا صالئ األػضاء أر أ ٠ى زا اخص

.لذ ؽمك ذف اإلفبدح اسبػذح ف رف١ش الذ اف

^^ال رسب صبؼ دػبئى

your brother :

Ammar Madkhana

*******************************************

the genentics summary

Documents