DNA Repair The human genome contains 3 billion base pairs . - PowerPoint Presentation

Slide1

DNA Repair

Slide2

The human genome contains 3 billion base pairs .

If we have an error one in a million this mean we will have 3000 errors during each replication cycle of the genome.

Slide3

The genome of a typical mammalian cell

accumulates many

thousands of lesions during a 24-hour period.

However, as a result of DNA repair, fewer than 1 in

1,000 becomes

a mutation. DNA is a relatively stable molecule

, but

in the absence of repair systems, the

cumulative effect

of many infrequent but damaging

reactions would

make life impossible.

Slide4

After

synthesis, the DNA may undergo some damages during the cell life-span, but naturally there are certain repair systems present inside the body that can provide protections against DNA damages.

The

rate of DNA repair is dependent on many factors, including the cell type, the age of the cell, and the extracellular

environment.

Slide5

A

cell that has accumulated a large amount of DNA damage, or one that no longer effectively repairs damage incurred to its DNA, can enter one of three possible states:

an irreversible state of dormancy, known as 

senescence

( getting old )

cell suicide, also known

as

 

apoptosis

 or 

programmed cell death

unregulated cell division, which can lead to the formation of a 

tumor

 that is 

cancerous

Slide6

The 2015 

Nobel Prize in Chemistry

 was awarded to 

Tomas

Lindahl

, 

Paul

Modrich

, and 

Aziz

Sancar

 

(

Turkish-American in the field of genetics, was born in

Mardin

in 1946 ), for

their work on the molecular mechanisms of DNA repair

processes.

 There are two types: 

nucleotide excision repair

 and 

base excision repair

Slide7

I

. Mismatch Repair System during DNA replication

1.Exonucleolytic proofreading of DNA polymerase usually occurring simultaneously with DNA replication. In these processes DNA molecules with single mismatched 3’ OH ends do not become effective templates because polymerase cannot extend when 3’ OH is not base paired. DNA polymerase has a separate

exonuclease

catalytic site that removes unpaired residues at the terminus and replace them by the correct base pair.

Slide8

2

. An

alternative DNA mismatch repair is a system which recognizes and repairs major insertion, deletion and

mis

-incorporation of bases

. During

DNA synthesis the newly synthesized (daughter) strand often includes errors and such defective copy of the mismatch repair gene could have serious consequences on human health.

Slide9

The mismatch repair system carries out the following corrections:

 Removes replication errors which are not

recognized

by the replication

machine.

 Detects structural changes in the DNA

helix.

The newly synthesized strand is preferentially nicked to be distinguished from the parental strand. Next step is the binding of mismatch proofreading complex at the defective base pair of the new strand, followed by removal of segment from this strand to be correctly replaced using the parental strand as a template

.

Slide10

II

. Repair

of DNA damage after DNA maturation

Main

Causes of DNA damage that occur after DNA synthesis:

1. Chemical

pollutants

2

. Radiation

Industrial chemicals such as vinyl chloride or hydrogen peroxide, and environmental chemicals such as polycyclic hydrocarbons found in smoke and tar create a large chemical modifications in DNA leading to the formation of oxidized bases, alkylated bases such as

methyl bases

or conversion of one base into another type (conversion of

cytidine

into

uridine

).

Slide11

Thermal disruption at elevated temperature increases the rate of

depurination

(loss of purine bases from the DNA backbone) and single strand breaks. For example, hydrolytic

depurination

is seen in the

thermophilic

bacteria, which grow in hot springs above 80 °C

.

Slide12

The main types of DNA damage caused by these environmental factors are:

base

loss

base

modification

strands breakage.

Slide13

Thymine

oxidation

Repair

of DNA damages

Despite

the exposure of DNA to large damaging environmental factors each day, very few damages actually have serious effects on human

chromosomal

DNA due to highly efficient repair mechanisms. An inactivation or loss of functions in these DNA repair systems may cause errors in replication and lead to genetic diseases such as :

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Fanconi

anaemia

 (

FA

)

It is

a rare 

genetic disease

. Among those affected the majority develop 

cancer

, most often 

acute

myelogenous

leukemia

, and 90% develop 

bone marrow failure

 (the inability to produce blood cells) by age 40. About 60–75% of people have 

congenital defects

, commonly 

short stature

, abnormalities of the skin, arms, head, eyes, kidneys, and ears, and developmental disabilities.

Slide16

Lynch syndrome

 (

HNPCC

 or 

hereditary

nonpolyposis

colorectal cancer

)

It is

an 

autosomal dominant

 genetic condition that has a high risk of 

colon

cancer

 as well as other cancers including 

endometrial

cancer

 (second most common), 

ovary

, 

stomach

, 

small intestine

,

hepatobiliary

tract

, upper 

urinary tract

, 

brain

, and

 

skin

. The increased risk for these cancers is due to inherited mutations that impair 

DNA mismatch repair

. It is a type of 

cancer syndrome

.

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Werner syndrome

 (WS)

It is also

known as "adult 

progeria

", is

a rare, 

autosomal

recessive

 

progeroid

syndrome

 (PS), which is characterized by the appearance of premature 

aging

. The

median and mean ages of death are 47–48 and 54 years,

respectively. The

main cause of death is 

cardiovascular disease

 or

cancer.

Slide18

Types of DNA repair systems

Base

Excision Repair (BER)

BER is a cellular mechanism that repairs damaged DNA throughout the cell cycle. It is

primarily responsible for removing small, non-helix distorting base lesions from

the genome

. BER is important for removing damaged bases that could otherwise

cause mutations

by

mispairing

or lead to breaks in DNA during replication. The repair

system containing

the following system:

Slide19

First

, a

glycosylase

enzyme recognizes a specific type of incorrect base., which

then cleaves

the N-

glycosyl

bond to remove the defective nitrogen base and generating

an

apurinic

or

apyrimidinic

(AP) site.

Different DNA

glycosylases

recognize different

types of

defective bases

.

Each DNA

glycosylase

is generally specific for one

type of lesion.

Uracil DNA

glycosylases

, for example, found in most cells, specifically remove from DNA the uracil that results from spontaneous deamination of cytosine. Mutant cells that lack this enzyme have a high rate of

G

C to A=T

mutations.

 

Slide20

2

. The AP sites generated by

glycosylase

action are then recognized by

AP endonuclease

, which cleaves the

phosphodiester

backbone immediately 5' to the AP site, leaving a 3'-OH and 5'-deoxyribose-phosphate terminus (incision step).

Slide21

3. The 5'

deoxyribose

phosphate is then removed by specific

exonuclease

called DNA

deoxyribo-phosphodiesterase

(

dRpase

), leaving a nick (gap).

4. The second strand is used as a template to fill in the gap. This process is carried out by a DNA polymerase and a DNA

ligase.

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UV-B light causes covalent cross-linking between adjacent thymine bases creating

cyclobutane

thymine dimmers

. Ionizing radiation such as that created by radioactive or x-rays causes breaks in DNA strands. When thymine dimers are present, the double helix is distorted (bent), as the

thymines

are pulled toward each other. Hydrogen bonding to adenines on the opposite strand is weakened .The distortion causes a loss of template information. In addition, it can prevent the advancing replication fork or inhibiting the process of RNA transcription.

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Fig. 10-13, p.252

UV irradiation causes dimerization of adjacent thymine bases

Slide25

Fig. 10-14, p.252

Oxidation

damage ( oxygen radicals in the presence of metal ions such as Fe

2

+ can destroy sugar rings in DNA,

breaking

the

strand.)

Slide26

Fig. 10-15, p.253

Missmatch

repair

in

E.coli

Slide27

BB

Fig. 10-16, p.254

Base –

excition

repair

Slide28

Nucleotide

Excision Repair (NER)

The

related nucleotide excision repair pathway repairs bulky helix-distorting lesions

1. Specific

endonuclease cleaves damaged DNA

on

either side of a lesion thereby producing a

short

gap.

2. Highly

processive

DNA polymerase fills in the

gap

and DNA ligase completes the repair

process

.

Slide29

Fig. 10-17, p.254

Nucleotide-excision

repair

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p.255

Recombination can be used to repair infrequent lesions

Slide32

Thymine dimer excision repair

system

A photo-reactivating enzyme system that can recognizes the thymine dimer and

in response

to visible light this enzyme system is stimulated to cleave the thymine

rings. The

system contains

UV

endonuclease

that

cleaves the damaged DNA on either side

of the

dimer to produce a short gap (about 100 nucleotides) on a single strand that can

be filled

by DNA polymerase using

opposite strand as a

template. Then the

DNA ligase

is used

to complete the repair

process.

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Xeroderma

pigmentosum

 

It is

a rare autosomal recessive 

genetic disorder

 of 

DNA repair

 in which the ability to repair damage caused by 

ultraviolet

 (UV) light is

deficient.

Slide35

Nearly 90% of these individuals develop skin carcinomas Most XP individuals also suffer from neurologic disorders including mental retardation. XP individuals are extremely sensitive to sunlight (UV light) and are unable to efficiently repair thymine dimers and other types of DNA damages

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END