Biochemistry-II - DNA Structure, Replication, and Repair - Quick Guides

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Study GuideBiochemistry-II–DNA Structure, Replication, and Repair1.DNA RepairWhy DNA Repair Is NecessaryDNA carries genetic information, but it is still achemical molecule, and like all chemicals, it can bedamaged by reactions.Any change that alters DNA sequence information is called amutation.Substances or agents that cause mutations are known asmutagens.Without repair systems, mutations would accumulate so rapidly that life could not be maintainedacross generations.Types of DNA MutationsSeveral kinds of mutations occur, depending on how the DNA sequence is changed.Figure 11. Transition MutationsAtransitionis a substitution within the same base class:•A–T↔G–C

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Study GuideExample:•Hydroxylamineremoves the amino group from deoxycytosine•Deoxycytosine becomesdeoxyuracil•During replication, uracil pairs with adenine•This convertsG–C → A–THydroxylamine is amonodirectional mutagenbecause it causes only one type of base change.2. Transversion MutationsAtransversionoccurs when:•Apurineis replaced by apyrimidine, or vice versaExamples:•A–T → T–A•A–T → C–GUltraviolet (UV) lightcan cause transversions, though it can cause other mutations as well.3. Frameshift MutationsFrameshift mutations occur when:•A base pair isinserted or deletedThis shifts the reading frame of the gene, often producing anonfunctional protein.Frameshifts are commonly caused byplanar intercalating agents, which insert between DNA bases.Large insertions and deletions also occur naturally.Ultraviolet Light as a MutagenUV radiation is a major environmental mutagen.

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Study Guide•Theozone layerabsorbs much UV radiation•Depletion of ozone (by CFCs) increases mutation riskAll DNA bases absorb UV light, becoming chemically reactive.Pyrimidine DimersUV light causes adjacent pyrimidines (especially thymine) to formpyrimidine dimers.•These dimers distort DNA structure•They blockDNA replication and transcription

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Study GuideFigure 2Spontaneous MutationsNot all mutations are caused by external agents.

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Study GuideSpontaneous mutationsarise from:•Errors during DNA replication•Normal chemical reactions•Heat (since higher temperature increases reaction rates)Thus, even normal cellular conditions can cause mutations.DNA Repair SystemsCells contain manyDNA repair mechanismsto counteract mutations.•Typical mutation rates areless than 1 per billion bases per generation•Humans have ~3 billion base pairs, so even identical twins differ by a few mutations•Viruses usually lack repair systems and rely on rapid replication insteadDirect Reversal of DNA DamageSome damage can be reversed directly.Example:•Alkylating agentsadd methyl groups to guanine•Specialized repair proteins remove the methyl group•The repair protein is then degradedThis restores the original DNA structure.Photoreactivation RepairUV-induced thymine dimers can be repaired directly byphotoreactivation.•The enzymeDNA photolyasebinds to thymine dimers•Visible light activates the enzyme•The dimer is split back into normal basesThis is a direct and efficient repair method.

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Study GuideExcision Repair: A General Repair SystemMany DNA lesions are repaired byexcision repair.Key steps:1.Damage is recognized (often by altered DNA shape)2.Anucleasecuts the DNA near the lesion3.The damaged segment is removed4.DNA polymerase Ifills in the missing bases5.DNA ligaseseals the strandThe intact complementary strand provides the correct sequence.Repair of Deoxyuridine in DNASpecial systems removedeoxyuridine (dU)from DNA.

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Study GuideFigure 3Sources of Deoxyuridine in DNAdU can appear in DNA due to:•Incorporation ofdUTPduring replication•Deamination of deoxycytidineIf dU remains in DNA:

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Study Guide•It pairs with adenine•This convertsG–C → A–Tafter replicationHow Cells Prevent dU-Induced MutationsCells use two main strategies:1.dUTPaseoConverts dUTP → dUMPoPrevents dUTP from being used by DNA polymerase2.Base-excision repairoRemoves uracil from DNA before replicationWhy DNA Uses Thymine Instead of UracilBoth thymine (T) and uracil (U) pair with adenine usingtwo hydrogen bonds.However, thymine has amethyl group, while uracil does not.This difference is crucial:•If cytosine deaminates → uracil → easily recognized and repaired•If5-methylcytosinedeaminates → thymine → hard to detectAs a result:•Repair systems cannot tell which strand is wrong•These sites becomemutation hot spotsDNA methylation therefore increases mutation risk at certain sequences.Key Takeaway•DNA damage leads tomutations•Mutagens include chemicals, UV light, and heat•Major mutation types:transition, transversion, frameshift

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Study Guide•UV light causespyrimidine dimers•Cells usedirect repair, photorepair, and excision repair•Special systems removeuracil from DNA•DNA uses thymine to improve mutation detection•Methylated DNA regions aremutation hot spots2.DNA Recombination and RepairWhen DNA Damage Is SevereSometimes DNA damage is so extensive that normal repair systems are not enough. In thesesituations, cells activate emergency mechanisms topreserve genetic information and survive.Two important strategies are:•SOS response (error-prone repair)•Recombinational repairBoth aim to keep the chromosome functional, even under extreme stress.2.1The SOS Response (Error-Prone Repair)TheSOS responseis a last-resort repair system.•It is activated when DNA damage is severe•The goal is toallow replication to continue•Accuracy is sacrificed for survival•Mutations are more likely, which is why it is callederror-prone repairAlthough imperfect, this response can prevent complete loss of genetic information.Recombinational Repair: Using Backup InformationRecombinational repairallows one DNA copy torepair another copyduring replication.

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Study Guide•Occurs at thereplication fork•One daughter chromosome supplies correct information to the other•Ensures that overall genetic information remains intactThis system relies heavily onhomologous recombination.Role of the RecA ProteinThe key protein in bacterial recombination and repair isRecA.•“Rec” stands for recombination•Cells lacking RecA cannot recombine DNA•Such cells are extremely sensitive toUV radiationRecA is astrand-exchange proteinthat initiates recombination.

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