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Overview

🌳 Concept tree

Lesson 2→DNA Structure, Replication and DNA Repair Enzymes

├── The structure of DNA

├── The data a model had to fit

├── The Watson–Crick model

├── Why the model fits the data

├── Worked example 3 — complementary strand

├── Worked example 4 — base percentages

├── Worked example 5 — a test for the type of nucleic acid
├── Why replicate?

├── The steps and the enzymes

├── Where replication starts

├── Summary of the enzymes

├── Worked example 6 — template and product

├── Worked example 7 — how many fragments?

├── Worked example 8 — speed of copying

├── DNA damage and repair

├── Worked example 9 — why does RNA virus mutate more?

├── Prokaryotes

├── Eukaryotes – chromatin and condensation

├── Comparison

├── Worked example 10 — packing ratio

├── The genome

├── Repetitive DNA

├── Worked example 11 — reasons

├── Definition

├── Kinds

├── Gamete and somatic mutations

├── Origin of mutations

├── Worked example 12 — classify

├── Key terms

└── Final recap

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The structure of DNA

🧬 3D Molecular Double Helix Model & Antiparallel Strands of DNA

D Bio/Geo Model→High-fidelity 3D structural model illustrating the Watson-Crick double helix: antiparallel sugar-phosphate backbones (5′ to 3′ vs 3′ to 5′), complementary base pairing (A=T with 2 hydrogen bonds, G≡C with 3 hydrogen bonds), and major/minor grooves.

By the early 1950s there was strong evidence that DNA carries the genetic information, and several teams tried to build a model of the molecule.
Any model had to accommodate the experimental data below.

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The data a model had to fit

Comparison aspect	Main idea	Keywords
DNA is made of nucleotides.	Each nucleotide has three parts: a five-carbon sugar deoxyribose a phosphate group covalently bonded to carbon 5′ of the sugar one of four nitrogenous bases covalently attached to carbon 1′ of the sugar: the single-ring pyrimidines – thymine (T) and cytosine (C) or the double-ring purines – adenine (A) and guanine (G)	threepartsfivecarbon
How nucleotides link.	The phosphate on the 5′ carbon of one nucleotide joins to the 3′ carbon of the sugar of the neighbouring nucleotide (a phosphodiester link). The chain of alternating sugar and phosphate is the sugar–phosphate backbone. The backbone is not symmetrical: it has direction (polarity) a free 3′ hydroxyl (–OH) at one end and a free 5′ phosphate at the other. The bases project sideways from the backbone	phosphatecarbonjoinssugar
Chargaff’s rules (base ratios).	In every DNA molecule the number of adenine = thymine and the number of guanine = cytosine (A = T G = C)	everymoleculenumberadenine
Franklin’s X-ray diffraction pictures (1952).	Rosalind Franklin sent X-rays through crystals of highly purified DNA. A regular molecule scatters X-rays in a pattern of spots whose analysis shows its shape. Her photographs showed that DNA is twisted into a helix the bases are perpendicular to the length of the fibre the sugar–phosphate backbone is on the outside with the bases inside and the diameter of the helix implied more than one strand	Rosalindsentraysthrough

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The Watson–Crick model

Putting all this information together
James Watson and Francis Crick produced the first acceptable model:

Two strands of DNA form a ladder shape. The sides of the ladder are the sugar–phosphate backbones; the rungs are pairs of bases.
Each rung is A paired with T, or G paired with C (complementary base pairing). Either base of a pair may be on either strand.
The base pairs are held together by hydrogen bonds two hydrogen bonds between A and T; three between G and C.
Because each rung is one double-ring purine paired with one single-ring pyrimidine, all rungs have the same width, so the two backbones stay at an equal distance along the whole molecule.
For the hydrogen bonds to form properly, the two strands must run in opposite directions (they are antiparallel): the 5′ end of one strand is next to the 3′ end of the other.
The whole ladder is twisted into a spiral with about ten base pairs per turn; because the spiral has two strands wound round each other, DNA is a double helix.

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Why the model fits the data

A = T and G = C follows directly from pairing rules.
The helix and the outside backbone match Franklin’s X-ray pictures.
The model also suggests how genetic information is copied each strand carries the information to build its partner. This leads to replication.

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Worked example 3 — complementary strand

Comparison aspect	Main idea	Keywords
Given	one strand reads 5′‑A‑A‑T‑C‑C‑3′. Find the partner	strandreadsFindpartner
Pair each base	A–T A–T T–A C–G C–G → 3′‑T‑T‑A‑G‑G‑5′. Note that the partner is written in the opposite direction read in the 5′→3′ direction it is 5′‑GGATT‑3′	Notepartnerwrittenopposite

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Worked example 4 — base percentages

Comparison aspect	Main idea	Keywords
Given	a DNA sample contains 28% adenine. Find the percentages of T G and C	samplecontainsadenineFind
•	A = T = 28% A + T = 56% so G + C = 44% and G = C = 22%
Hydrogen bonds	a segment of 100 base pairs with 30 A–T pairs and 70 G–C pairs has (30×2) + (70×3) = 270 hydrogen bonds. Segments rich in G–C are more heat-stable	segmentbasepairsSegments

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Worked example 5 — a test for the type of nucleic acid

A sample of nucleic acid has A = 21%, T = 29%, G = 24%, C = 26%.
Here A ≠ T and G ≠ C, so the sample is not a double helix; with thymine present it is not RNA either.
It is single-stranded DNA.

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Why replicate?

Before a cell divides, its DNA must be copied (replicated) so that each daughter cell receives a complete set of the genetic information.
Watson and Crick pointed out that the structure itself provides the method.
Because the two strands are complementary, the base sequence of each strand automatically specifies its partner.
For example, if one strand runs 5′‑A‑A‑T‑C‑C‑3′, the partner must be 3′‑T‑T‑A‑G‑G‑5′.
If the two strands are separated, each can act as a template (mould) for a new complementary strand.
Experiments later proved this.
Each new DNA molecule thus contains one old strand and one new strand (semi-conservative replication).

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The steps and the enzymes

Replication needs the coordinated action of many enzymes and proteins.

Comparison aspect	Main idea	Keywords
•	Unwinding the double helix	Unwindingdoublehelix
Helicase	moves along the helix and breaks the hydrogen bonds between paired bases separating the strands. The Y-shaped region where the strands separate is the replication fork. It exposes the bases so they can pair with new nucleotides	movesalonghelixbreaks
DNA polymerase	builds the new strand. It adds nucleotides one at a time to the 3′ end of the growing strand each incoming nucleotide must pair with the exposed base on the template strand	buildsstrandaddsnucleotides
Primase	makes short pieces of RNA called primers that pair with the template. DNA polymerase cannot start a strand alone it can only extend an existing 3′ end so it needs the primer	makesshortpiecescalled
Leading and lagging strands.	DNA polymerase works only in one direction: it reads the template from 3′ to 5′ and builds the new strand from 5′ to 3′. The two template strands are antiparallel so: On the template that runs 3′→5′ in the direction of the fork’s movement the polymerase follows the helicase continuously and makes a continuous new strand in the 5′→3′ direction: the leading strand. On the other template (5′→3′) the polymerase cannot move continuously in the direction of the fork. The new strand is therefore made in short pieces called Okazaki fragments each made 5′→3′ (away from the fork) each needing its own primer. This is the lagging strand	polymeraseworksdirectionreads
Joining the fragments.	After replication of a fragment the RNA primers are removed and a type of DNA polymerase fills the gaps with DNA nucleotides. DNA ligase then joins the Okazaki fragments into a continuous strand	Afterreplicationprimersremoved

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Where replication starts

Comparison aspect	Main idea	Keywords
Eukaryotes	each chromosome contains one long DNA molecule replication starts at hundreds or thousands of origins along it at once which makes copying quick	chromosomecontainslongmolecule
Prokaryotes	DNA is a circular double helix attached to the plasma membrane at one point that attachment point is where replication starts	circulardoublehelixattached

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Summary of the enzymes

Enzyme	Job
Helicase	Unwinds and separates strands by breaking H-bonds forms the replication fork
Primase	Makes short RNA primers
DNA polymerase	Adds DNA nucleotides to 3′ end of new strand replaces primers with DNA
DNA ligase	Seals the gaps between Okazaki fragments (and in repair)

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Worked example 6 — template and product

A template strand reads 3′‑TACGGATC‑5′.
The new strand is 5′‑ATGCCTAG‑3′.
It is made in the 5′→3′ direction, adding each nucleotide to its 3′ end.

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Worked example 7 — how many fragments?

A lagging strand is built from 6 Okazaki fragments.
How many primers and ligations are needed on that strand?
Each fragment needs its own primer (6 primers).
After the primers are replaced by DNA, ligase joins 6 fragments by 5 joints.
(The leading strand needs only one primer at the origin.)

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Worked example 8 — speed of copying

Why can a human cell copy its 2 metres of DNA in a few hours?
Because replication starts at many origins at the same time in each chromosome and moves in both directions from each.

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DNA damage and repair

All biological polymers (starch, proteins, nucleic acids) can be damaged by the cell’s own heat and the watery environment.
DNA is no exception.

It is estimated that about 5,000 purine bases (A and G) are lost from the DNA of each human cell every day because heat breaks the covalent bonds joining them to deoxyribose.
Chemicals and radiation also damage DNA.
Any damage can change the information and produce harmful changes in the cell’s proteins.

Although thousands of changes occur daily, only two or three permanent changes accumulate in a cell’s DNA per year.
Nearly all damage is removed by about 20 kinds of DNA repair enzymes.
Working together, the enzymes recognise and cut out a damaged region and replace it with nucleotides complementary to those on the opposite (undamaged) strand, then ligase seals the gap.
Repair depends on having two copies of the information, one in each strand.

While one strand is undamaged it serves as a template to repair its partner.
Damage is only permanent if both strands are damaged at the same place at the same time.
By contrast, single-stranded RNA genomes (some viruses) have no second copy and cannot be repaired; such viruses show high rates of genetic change.
So the double helix is vital for genetic stability.

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Worked example 9 — why does RNA virus mutate more?

A single-stranded RNA genome has no complementary strand to use as a template
so damaged or miscopied bases remain
hence the virus changes quickly (this is why flu vaccines have to be updated).

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Prokaryotes

The genetic material is one double helix of DNA whose ends are joined, forming a circle.
If the DNA of the bacterium Escherichia coli were stretched out, it would be about 1.4 mm long, while the cell is only about 2 micrometres long. The circle is therefore folded many times and occupies a "nuclear" region of about one-tenth of the cell volume (no nuclear envelope).
It is attached to the plasma membrane at one point, where replication begins.
Many bacteria carry additional small circular DNA molecules called plasmids. A bacterium replicates its plasmids at the same time as its main DNA. Plasmids are valuable in genetic engineering: scientists introduce artificial plasmids into bacteria to obtain many copies of them.
DNA of mitochondria and chloroplasts, and the plasmids of yeast, are circular like prokaryotic DNA and are not combined with proteins the way eukaryotic nuclear DNA is.

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Eukaryotes – chromatin and condensation

Chromosomes are visible during cell division. Each contains one DNA molecule extending from end to end, coiled and folded many times. DNA is combined with proteins to form chromatin, which contains roughly equal amounts of DNA and protein.
Two groups of chromosomal proteins Histones – a well-defined group of small structural proteins rich in the basic amino acids arginine and lysine. At cell pH these have positively charged R groups, so they bind firmly to the negatively charged phosphate groups of DNA. Histones are abundant in all cells. Non-histone proteins – a varied group: structural proteins that help organise DNA in the nucleus, and regulatory proteins that decide whether the DNA code is used to make RNA, proteins and enzymes.
The packing problem. A human somatic cell has 46 chromosomes; if all their DNA were stretched out it would be about 2 m long, yet the nucleus has a diameter of only 2–3 micrometres. Histones and other proteins pack the DNA:
1. DNA double helix is wound around clusters of histones, forming a string of beads called nucleosomes (shortens the DNA about tenfold; it must still be packed about 100,000 times to fit).
2. The nucleosome string coils (coiled nucleosomes).
3. These are folded into loops, held in place by non-histone structural proteins, forming chromatin.
4. Chromatin condenses further into condensed chromatin, which forms the chromatid/chromosome (most compact in prophase of cell division).
When DNA is in a condensed state enzymes cannot reach it. For DNA to act as a template for DNA or RNA synthesis, it must unwind at least to the nucleosome-string level.

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Comparison

Point	Prokaryote	Eukaryote
Shape	Circular, one main molecule + plasmids	Linear, several chromosomes
Location	Nuclear area (no envelope)	Inside nucleus (plus mitochondria chloroplasts)
Proteins	Not complexed with histones	Complexed with histones – chromatin
Replication origins	One	Many
Mostly coding?	Yes, most is genes	Only a small fraction codes for protein

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Worked example 10 — packing ratio

For E. coli, 1.4 mm of DNA fits into a 2 μm cell: 1.4 mm = 1400 μm, so the DNA is 700 times longer than the cell.
For human DNA, 2 m in a 3 μm nucleus: 2 m = 2,000,000 μm, about 670,000 times the diameter.

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The genome

The genome (gene content) is all the genes – so all the DNA – in a cell of an individual.

Many genes carry instructions for making proteins. Others specify the sequence of nucleotides in ribosomal RNA (rRNA), used to build ribosomes, and transfer RNA (tRNA), which carries amino acids in protein synthesis.
In prokaryotes, the genes for RNA and protein make up most of the genome.
In eukaryotes, only a small percentage of DNA codes for proteins; the rest is non-coding (not transcribed to make RNA or proteins).

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Repetitive DNA

Most genes occur in one or a few copies. But a eukaryotic cell holds many (often hundreds) of copies of the genes for rRNA and histones, since the cell needs these in large amounts. Many copies speed up the production of new ribosomes and histones.
Eukaryotic genomes also contain a great deal of other non-coding DNA (including satellite DNA). The amount of DNA in a species bears little relation to the complexity of the organism or the number of proteins it makes. Example: the largest known genome belongs to a salamander, with about 30 times the DNA of a human cell, though it makes fewer proteins.
Some non-coding DNA may maintain the structure of chromosomes; some regions mark where RNA synthesis should start. These are promoters, at the beginning of each gene, and are important in protein synthesis.

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Worked example 11 — reasons

Why does a salamander have 30 times more DNA than a human but fewer traits?
Because most of the extra DNA is non-coding or repetitive and does not specify proteins; the number of traits depends on the number of coding genes, not on total DNA.

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Definition

A mutation is a sudden change in the hereditary factors controlling certain traits, which leads to a change in those traits in the organism.
A mutation is "true" if it is transmitted through the generations.
We must distinguish it from changes caused by environmental effects or by the segregation and recombination of genes, which do not change the hereditary factor itself.

Most mutations are harmful – for instance deformities in humans, or sterility and low crop yield in plants.
Rarely, a mutation is beneficial, and people try to cause useful ones artificially.
Examples the American farmer who found a short, curved-legged lamb that could not jump fences, bred it and produced the Ancon sheep strain; and mutations induced in crops to increase yield.

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Kinds

Gene (point) mutations. Chemical changes within the gene, mainly in the arrangement of nitrogenous bases in DNA.
The changed gene gives a different protein, and so a new trait.
The change is often from the dominant to the recessive state (rarely the reverse).
A gene mutation can happen by substitution (replacing), deletion, or addition (insertion) of nucleotides.
2. Chromosomal mutations.
(a) Change in chromosome number:

Comparison aspect	Main idea	Example	Keywords
Aneuploidy	gain or loss of single chromosomes during meiosis	Klinefelter syndrome (44 + XXY) one extra chromosome Turner syndrome (44 + XO) one chromosome fewer	gainlosssinglechromosomes
Polyploidy	whole sets of chromosomes are multiplied due to non-separation of chromatids after centromere division and failure of a membrane to form between daughter cells. Types: 3N 8N up to 16N. Polyploidy is common in plants: each gene is present in many copies so its effect is stronger – the plant is taller and organs (flowers fruits) larger. Many crops are tetraploid (4N) – cotton wheat apple grapes pears strawberries. It is rare in animals because sex determination needs a delicate balance between autosomes and sex chromosomes it occurs in some hermaphrodite snails and worms. Triploidy in humans is lethal (miscarriage) though polyploid cells occur normally in some liver and pancreas cells. (b) Change in chromosome structure: a piece breaks off turns through 180° and rejoins (inversion) two non-homologous chromosomes exchange segments (translocation) a small segment is lost (deletion) or gained (duplication). The gene order is altered	—	wholesetschromosomesmultiplied

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Gamete and somatic mutations

Comparison aspect	Main idea	Keywords
Gamete (germ-line) mutation	occurs in reproductive cells so the new trait appears in the embryo and is inherited (sexually reproducing organisms)	occursreproductivecellstrait
Somatic mutation	occurs in body cells so the symptom appears in the organ whose cells mutated. It is important in vegetatively propagated plants where a new branch with a new trait may appear and can be cut and propagated if the trait is desirable	occursbodycellssymptom

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Origin of mutations

Comparison aspect	Main idea	Example	Keywords
Spontaneous	occur naturally without human interference rare caused by environmental factors	ultraviolet and cosmic rays and various chemicals. They are important for evolution	occurnaturallywithouthuman
Induced	produced by humans to obtain desired changes. Agents: gamma rays ultraviolet rays chemicals	mustard gas colchicine nitrous acid. In plants treatment kills growing-tip cells new tissue regenerates under the dead cells and includes some polyploid cells. Most induced mutations are harmful but breeders select the useful ones: for example fruit trees with sweeter or seedless fruit and mutants of the mould Penicillium that make much more antibiotic	producedhumansobtaindesired

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Worked example 12 — classify

(a) A person with 47 chromosomes, 44 + XXY → chromosomal mutation (number), Klinefelter syndrome, gamete mutation in the parent. (b) A strawberry plant with 4N → polyploidy, giving bigger fruit. (c) A bud on an apple tree develops a branch with red instead of green apples → somatic mutation, kept by grafting or cuttings. (d) Replacement of one base in a gene → gene (point) mutation.

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Key terms

genetic material, bacterial transformation, virulent, bacteriophage, deoxyribonuclease, nucleotide, purine, pyrimidine, sugar–phosphate backbone, Chargaff’s rule, X-ray diffraction, double helix, antiparallel, replication fork, helicase, DNA polymerase, primase, primer, leading and lagging strands, Okazaki fragment, DNA ligase, DNA repair, plasmid, histone, nucleosome, chromatin, genome, repetitive DNA, promoter, mutation (gene, chromosomal, polyploidy, aneuploidy, gamete, somatic, spontaneous, induced).

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Final recap

Griffith (transformation), Avery (DNase control), Hershey–Chase (³²P/³⁵S) and constant DNA content show that DNA is the genetic material (RNA in some viruses). 2. DNA: two antiparallel strands, sugar–phosphate outside, A=T (2 H-bonds), G≡C (3 H-bonds), ten bp per turn. 3. Replication is semi-conservative: helicase → primase → DNA polymerase (leading and lagging strands, Okazaki fragments) → ligase. 4. Repair uses the undamaged strand as template. 5. Prokaryotic DNA is circular; eukaryotic DNA is wrapped around histones in nucleosomes and packed into chromatin and chromosomes. 6. Genome = all DNA of an individual; most eukaryotic DNA is non-coding. 7. Mutations: gene or chromosomal, spontaneous or induced, gamete or somatic.

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Part 32

📖

🔍 In-Depth Explanations, Deductions & Multi-Book Insights:

DABOUR HUB ACADEMY • EGYPTIAN HIGH SCHOOL (THANAWEYA AMMA)
EXPLANATION Lesson 2: DNA Structure, Replication and DNA Repair Enzymes
Course Biology (Senior 3) | Chapter 5 – Molecular Biology – DNA Structure and Function | Official Ministerial Syllabus 2026/2027
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1. Academic Lesson Overview & Pedagogical Objectives

Franklin's X-ray crystallography
Watson and Crick's double helix model
semi-conservative replication enzymes (Helicase
Polymerase
Ligase)
and DNA repair mechanisms.

2. Hierarchy Classification Tree (Cognitive Concept Map)

Below is the hierarchical structural tree organizing the conceptual core of this lesson:

DNA Double Helix & Replication

├── 1. Watson-Crick Model (1953)

Comparison aspect	Main idea	Keywords
│ ├── Antiparallel Strands	5' to 3' vs. 3' to 5'
•	│ ├── Sugar-Phosphate Backbone on exterior Nitrogenous bases inward perpendicular to axis	SugarPhosphateBackboneexterior
│ └── Base Pairing	A = T (2 Hydrogen bonds) G ≡ C (3 Hydrogen bonds)	Hydrogenbonds

├── 2. DNA Replication Enzymes

│ ├── HelicaseUnwinds and separates the double helix by breaking hydrogen bonds

│ ├── DNA PolymeraseBuilds new strand strictly in 5' → 3' direction (Continuous on leading, Discontinuous on lagging)

│ └── DNA LigaseLinks Okazaki fragments on lagging strand; repairs chemical DNA lesions

└── 3. DNA Repair & Mutations

├── Causes of LesionsThermal heat (~5000 purine bases lost daily!), radiation, chemicals

└── Repair Enzymes (20 enzymes)Identify damaged base, excise it, and replace using intact opposite strand as template!

3. The Master Teacher's Blackboard & Exam Rules

Comparison aspect	Main idea	Keywords
•	Extracted high-yield rules golden equations and trap warnings from top Egyptian teachers	Extractedhighyieldrules
• RULE 1	DNA Polymerase synthesizes ONLY in the 5' → 3' direction	Polymerasesynthesizesdirection
• RULE 2	In any double-stranded DNA: %A = %T %G = %C and (A+G) = (T+C) = 50% (Purines = Pyrimidines)	doublestrandedPurinesPyrimidines
• RULE 3	Repair enzymes REQUIRE an intact opposite strand if both opposite bases are damaged simultaneously the lesion becomes a permanent mutation	RepairenzymesREQUIREintact
• TRAP	One full turn of DNA double helix contains 10 base pairs (20 nucleotides total)	fullturndoublehelix

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