02 DNA Structure and Replication

8/14/2019 02 DNA Structure and Replication

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Vasudevan 1

DNA Structu reAndRepl icati on


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Purines : Adenine, GuaninePyrimidines : Thymine, Cytosine

Bases- Purines

Pyrimidines


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O

HOH

OH

P O

O

O

O

H

OH

P OO

O

O

H

OH

P

OH

O O

O-H2C

_

O-H2C

_

O-H2C

_5' phosphate end

3' OH end

Adenine

Cystosine

Thymine

OH

3

H

Base + Deoxy ribose = Nucleoside

2


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Vasudevan 4

O

HOH

OH

P O

O

O

O

H

OH

P OO

O

O

H

OH

P

OH

O O

O-H2C

_

O-H2C

_

O-H2C

_5' phosphate end

3' OH end

Adenine

Cystosine

Thymine

OH

3

Base + Deoxy ribose + Phosphoric acid

= Nucleotide


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O

HOH

OH

P O

O

O

O

H

OH

P OO

O

O

H

OH

P

OH

O O

O-H2C

_

O-H2C

_

O-H2C

_5' phosphate end

3' OH end

Adenine

Cystosine

Thymine

OH

3

Phospho

Diester

linkage


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O

HOH

OH

P O

O

O

O

H

OH

P OO

O

O

H

OH

P

OH

O O

O-H2C

_

O-H2C

_

O-H2C

_5' phosphate end

3' OH end

Adenine

Cystosine

Thymine

5-T-C-A-3

Polarity

Phospho

Diester

linkage


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5 end 3 end

Phosphate

bonds

Bases

jutting

inside

Double

Helix


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Base pairing rule

A to T

G to C

Nucl eoti d

Hydrogenbondsbetweenbases


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Watson

1962

Crick

1962

Wilkins

1962

Edwin

Chargaff

1905- 2002

Rosalind

Franklin

1921-1958


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Watson-Crick Model of DNA

1. Right handed Double Helix

2. Base pairing rule, A toT; G to C

by Hydrogen bonding

3. Antiparallel 5 33 5

4. 10 base pairs form one spiral


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DNA wraps twice aroundhistone octamer to form

one nucleosome

DNA strand

Cor e histones as octamer


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1 DNA double helix

2 FormsNucleosomes

3 Forms Supercoil

4 Condensed tochromatin

5 Finally condensed as chromosomes


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1 DNA double helix

2 FormsNucleosomes

3 Forms Supercoil




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1 DNA double helix

2 FormsNucleosomes

3 Forms Supercoil




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1 DNA double helix

2 FormsNucleosomes

3 Forms Supercoil




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1 DNA double helix

2 FormsNucleosomes

3 Forms Supercoil




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Inactiv ation of DNADuringDif ferenti ationAll human cells are derived from a

single cell, the zygote. Therefore,

all cells contain the same geneticinformation.

In a cell, about 90% DNA arepermanently inactive.

Diff erentiat ion .


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Intr ons, Exons, C istr onsOnly about 10% of the human DNAcontains genes; the rest silent

areas.

The segments of the gene codingfor proteins are called exons (expressed regions).

They are interspaced in the DNAwith stretches of silent areas,

called introns (intervening areas).


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The primary transcripts contain

intron sequences;

which are later removed to

produce mature mRNA.

Introns are not translated.

CISTRONS


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REPLICATION

Synthesis of new DNA strandon the basis of template strand

Semiconservativereplication

A new complementary strand issynthesised over the old template


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Parent cell

DNA

First

generation

Second

generation

Meselson (Left)

and Stahl (Right)


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Conservative

replication(theoretical;

but actually

not taking place)

Semi -conservati verepl icati on(actual )


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Conservative

replication(theoretical;

but actually

not taking place)

Semi -conservati verepl icati on(actual )


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Old strands

Parent strands

Partially

unwound

New strands madeBased on

Base Pairing rule

Old New Old New


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Salient features of Replication

1.Each strand serves as a TEMPLATE

over which new COMPLEMENTARY

strand is synthesised

2. Base parining rule, A with T; G to C

3. Polymerisation of the newstrand is taking place from 5 to 3

direction


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5 3

OH

DNAPolymerase (DNAP)

5 in number; alpha is main enzyme

Arthur Kornberg

NP 1959


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5 3

C

OH

DNAPolymerase action


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5 3

OH

T



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5 3



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RNA primer is needed for DNA synthesis

primaseRNA primer

Old DNA strand

DNA polymerase

New DNA strandAnother DNAP

Completed new DNA strand


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Old DNA strand

DNA polymerase



RNA primer

RNA primer primase


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Old DNA strand

DNA polymerase



RNA primer


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RNA primer is needed for DNA synthesis

Old DNA strand

DNA polymerase




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DNA uncoils RNA primer

New DNA

Replication bubble (Replication fork)

5

5

3

3


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3

5

3

Di recti onof forkmovem ent

5

3

Leadi ng s trandShort RNA pr imerOkazaki fragment

Poi nt of joini ngaf terremovi ng RNA prmerLaggi ng st rand

3

Old strand

5

Lagging strand and Okazaki pieces


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3

5

3


5

3



3

Old strand

5



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3

5

3


5

3



3

Old strand

5

3

5



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3

5

3


5

3

Leadi ng s trandShort RNA pr imerOkazaki fragmentOrOkazaki piecesoi nt of joini ngaf terremovi ng RNA prmer

Laggi ng st rand3

Old strand

53

5



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3

5

3


5

3


Poi nt of joini ngaf terremovi ng RNA pri merLaggi ng st rand

3

Old strand

5

5



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3

5

3


5

3



3

Old strand

5

5



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Summary of DNA replication

1. Unwinding of parental DNA toform a replication fork.2. RNA primer complementary to

the DNA template is synthesised

by RNA primase.3. DNA synthesis is continuous inleading strand (towards replication

fork) by DNA polymerase.4. DNA synthesis is discontinuous inlagging strand (away from the

fork), as Okazaki fragments.

S f


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5. In both strands, the synthesis isfrom 5' to 3' direction.

6. Then the RNA pieces are removed;the gaps filled by deoxynucleo-

tides and the pieces are ligated by

DNA ligase.

7.Proof reading is done by the DNApolymerase.

8. Finally organised into chromatin.

Summary of DNA replication


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Old template strand

containsmethylated

bases; so wrong

base could beidentified

NUCLEOTIDE EXCISION

REPAIR (NER) MECHANISM


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A portion

around

that area is cut

and removed by

endonuclease

Old template strand

contains methylated

bases; so wrong base

could be identified

NUCLEOTIDE EXCISION



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A portion around

that area is cut

and removed by

endonuclease

Gap is filled with

correct base

sequences byDNA polymerase

Old template strand

contains methylated


could be identified

NUCLEOTIDE EXCISION



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Old template strand

contains methylated


could be identifiedA portion around

that area is cut and

removed by

endonuclease

Gap is filled with

correct base

sequences by DNA

polymerase

Finally DNA

ligase

seals the nicks


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Diseases associated with

DNA repair mechanisms

1. Xeroderma Pigm en tosum :Defective NER mechanism;

sensitivity to UV light; skin cancers

2. Ataxi a Telangectasi a :defective ATM gene; sensitivy to UV

light; lymphoreticular neoplasms

3. Fanconi 's Anemi a: Defectin DNA repair; increased occurrence

of cancer DNAP coul d not r epl icate thi s area


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3'(Tel omer e)

5' Tel omerase

RNA templ ateinsidetel omer ase

New tel omere repeat

RNA produced bytel omer ase acts asri merDNA pol ymerasecompl etes

laggi ng str and DNAP coul d not r epl icate thi s area


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3'5' Tel omerase



RNA produced bytel omer ase acts asri merDNA pol ymerasecompl etes

laggi ng str and

(Tel omer e)

DNAP coul d not r epl icate thi s area


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3'5' Tel omerase



RNA produced bytel omer ase acts asri merDNA pol ymerasecompl eteslaggi ng str and

(Tel omer e)

Inhibitors of DNA replication


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Inhibitors of DNA replication

1. Anti bacterial agentsa)Ciprofloxacin

Inhibits Bacterial DNA gyrase

b)Nalidixic acid do

c)Novobiocin do


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2. An ticancer agents

a)Etoposide Humantopo-isomerase

b)Adriamycin do

c)Doxorubicin do

d)6-mercaptopurine Human

DNA polymerase

e)5-fluoro uracil do


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What enz ymes are requi red f orDN A repl icati on?DNA pol ymeraseTopo iso mer aseDNA ligase


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Repl icat ion is in whi ch di rect ion?Pol ymeri sat ion of the new strandof DN A is f rom 5 to 3 di recti onWhat is semi -conservativenatur e of repl icati on?In the daughter c ell , one strandis de rived from the mother cel l;whi le the other strand is n ewlysynthesi sed


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What is semi -di sconti nuou snatur e of repl icati on?In the l eadi ng str and, therepl ication is co ntinuous;but in the laggin g strand,repl ication is taki ng placein smal l pi eces.


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What is l aggi ng str and?The stran d i n whi ch rep licati onis dis- conti nuous is cal ledLaggi ng st randWhat are O kaz aki fragments?The saml l DN A m ole culesattached to its own primer RN Ain the laggi ng st rand are call edOkazaki piec es.


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Name the drug s wh ich inhi bi tDN A repl icati on in prokaryotesCi prof loxaci ne, Novobi oci n

Name some anti cancer drugswhi ch inhibi t DN A re pl icati on i nammal ian cel ls5- fluorouraci l6-mercaptopurineCytosi ne a rabi nosi de

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02 DNA Structure and Replication