i want 25 multiple choice questions with their model answer below each question that covers different aspects of the all following information about : Repair
An Overview
• Because each cell contains only one or two copies of its DNA, the DNA sequence is highly protected from harm.
• DNA is a relatively stable molecule, but Earth’s natural environment is quite toxic, and damage to DNA is inevitable.
• DNA can also be altered by mistakes made during its own replication or recombination.
• Damage and sequence alterations to DNA are often quickly repaired, but when they are not, the DNA becomes permanently altered and harbors a mutation.
• Mutations are changes in DNA sequence, and when mutations occur in germ-line cells, these changes are inheritable.Continue..
• A cancer cell has mutations that prevent cell death, resulting in loss of
cell cycle control and unregulated cell division, which leads to
malignant tumors that can end the life of the entire organism.
• The cell has a limited amount of time to fix the initial alteration and
restore the DNA to its normal sequence, before replication converts
the alteration into a mutation that will be passed on to the next
generation.Continue..
• Mutation
• Somatic mutations : occur in somatic cells and only
affect the individual in which the mutation arises.
• Germ-line mutations: alter gametes and passed to
the next generation.DNA Damage
• Errors can occur during replication, an error can occur
for every 30,000 bases.
“despite the proofreading system”.
• In addition, there are some damaging agents like
environmental insults.
• Maintenance of the integrity of DNA molecule is very
important for the survival of species or organisms.
6• Chemical mutagens • Radiation
Agents that Damage DNA
• Radiations
• Highly reactive oxygen radicals produced during normal cellular respiration as well as by other biochemical pathways
lonizing radiation such as gamma rays and x-rays
• Ultraviolet rays, especially the UV-C rays (~260 nm) that are absorbed strongly by DNA but also the longer-wavelength UV-B that penetrates the ozone shield
Agents that Damage DNA
• Chemicals in the environment .
• Aromatic hydrocarbons, including some found in cigarette smoke
• Plant and microbial products, e.g. the Aflatoxin produced in moldy peanuts
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• Chemicals used in chemotherapy, especially chemotherapy of cancers.
Types of DNA damage
Type of Damage
S.No
1)
2)
3)
4)
Examples
A.Depurination
B.Deamination of cytosine to uracil
Single-base alteration
C.Deamination of adenine to hypoxanthine
D.Alkylation of base
E.Insertion or deletion of nucleotide
F.Base-analog incorporation
Two-base alterations
A. UV light-induced thymine-thymine (pyrimidine) dimer
Chain breaks
A. lonizing radiation
B. Radioactive disintegration of backbone element)
C. Oxidative free radical formation
Cross-linkage
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A. Between bases in same or opposite strands
B. Between DNA and protein molecules (eg, histones)
Deoxy- ribose
a
CH H
Ultraviolet (UV) light (254nm)
Deoxy ribose
P
Deaky ribose
CH
Two-base alterations
Deoxy- ribose
H
H
P
Types of DNA Repair
i) Base excision repair (BER)
ii) Nucleotide excision repair (NER),
iii) Mismatch repair (MMR) and
iv) Strand break repairs.
In these reactions a nucleotide segment containing base damage, double-helix distortion or mispaired bases is replaced by the normal nucleotide sequence in a new DNA polymerase synthesis process.
• All of these pathways have been characterized in both bacterial and eukaryotic organisms.
i)	Base Excision Repair (BER
Base excision-repair of DNA
. The enzyme uracil DNA glycosylase removes the uracil created by spontaneous deamination of cytosine in the DNA.
. An endonuclease cuts the backbone near the defect
An endonuclease removes a few bases
The defect is filled in by the action of a DNA polymerase and
i)	The strand is rejoined by a ligase.
ii)	Types of lesions repaired by BER
iii)	• Oxidative lesions • Deoxyuracil: from misincorporation of dU or deamination of dC-->dU
iv)	• Various alkylation products • Spontaneous depurination (esp. G) yield abasic sitesNucleotide excision repair (NER)
v)	• Recognizes bulky lesions that block DNA replication (i.
vi)	e. lesions produced by carcinogens)--example, UV
vii)	pyrimidine photodimers
viii)	• Common distortion in helix
ix)	• Incision on both sides of lesion
x)	• Short patch of DNA excised, repaired by
xi)	repolymerization and ligation
xii)	• In E. coli, mediated by UvrABC excinuclease

xiii)	• Many more proteins involved in eukaryotes
xiv)	• Defects in NER underlie Xeroderma pigmentosumNUCLEOTIDE EXCISION REPAIR
xv)	• Exposure to UV radiation induces covalent joining of 2 adjacent
xvi)	thymine bases.
xvii)	• These TT dimers result in arrest of DNA replication.
xviii)	17NUCLEOTIDE EXCISION REPAIR
xix)	Xeroderma pigmentosum (XP)
xx)	Xeroderma pigmentosum (XP) is an autosomal recessive genetic disease.
xxi)	The clinical syndrome includes marked sensitivity to sunlight (ultraviolet) with subsequent formation of multiple skin cancers and premature death.
xxii)	The risk of developing skin cancer is increased 1000- to 2000-fold.
xxiii)	The inherited defect seems to involve the repair of damaged DNA, particularly thymine dimers.
xxiv)	Cells cultured from patients with xeroderma pigmentosum exhibit low activity for the nucleotide excision-repair process
xxv)	MISMATCH Repair
xxvi)	• Replication errors that escape the proofreading activity
xxvii)	mismatch in one or several bases. • Repair is mediated by Mut proteins in two steps:
xxviii)	1. Identifying the strand with the mismatch 2. Repair procedure
xxix)	iii) Mismatch repair (MMR)
xxx)	This mechanism corrects a single mismatch base pair (eg, C to A rather than T to A) or a short region of unpaired DNA.
xxxi)	The defective region is recognized by an endonuclease that makes a single-strand cut at an adjacent methylated GATC sequence.
xxxii)	The DNA strand is removed through the mutation, replaced, and religated
xxxiii)	Mismatch repair
xxxiv)	1. In prokaryotic MMR , the degree
xxxv)	of methylation
xxxvi)	identifies the “correct” strand. The parental strand is more highly methylated than the daughter strand immediately after
xxxvii)	replication and is
xxxviii)	assumed to be the correct strand. [ Note: Mutations to human MMR proteins result in hereditary
xxxix)	nonpolyposis colorectal cancer ( HNPCC ).] 23Double strand break repair
xl)	• Double strand breaks occur due to:
xli)	1. Ionizing radiation 2. Oxidative free radicles 3. Chemotherapeutic drugs.
xlii)	B) Repairing Strand Breaks
xliii)	ii) Double-Strand Break Repair
xliv)	There are two mechanisms by which the cell attempts to repair a complete break in a DNA molecule:
xlv)	• 1) Direct joining of the broken ends. This requires proteins that recognize and bind to the exposed ends and bring them together for ligating. This type of joining is also called Nonhomologous End-Joining (NHEJ). A protein called Ku is essential for NHEJ.
xlvi)	Brochemestry for Medics Lecture Nkes
xlvii)	B) Repairing Strand Breaks
xlviii)	• Errors in direct joining may be a cause of the various translocations that are associated with cancers. Examples:
xlix)	• Burkitt's lymphoma
l)	Philadelphia chromosome in chronic myelogenous leukemia (CML)
li)	• B-cell leukemia. Double strand break repair
lii)	• Homologous recombination: between homologous chromosomes. No loss of DNA as we can use homologous chromosome as template to replace the lost bases.
liii)	28
• Occurs in late S-phase or in G2 phase.Either
B) Repairing Strand Breaks
2) Homologous Recombination. Here the broken ends are repaired using the information on the intact
Either
homologous chromosome
liv)	same chromosome if there are duplicate copies of the gene on the chromosome oriented in opposite directions (head-to-head or back-to-back).
Two of the proteins used in homologous recombination are encoded by the genes BRCA1 and BRCA2.
• Inherited mutations in these genes predispose women to breast and ovarian cancers.