Unit 3 Nucleic acids and DNA replication
Key unit competence: Explain the structure of chromosomes, how DNA is packaged within them, and describe the process and biological significance of DNA replication.
Key ideas
- Chromosomes are made of chromatin: DNA wound around histone proteins. DNA wraps around groups of 8 histones to form nucleosomes ("beads on a string"), which coil into 30 nm fibres, loops and, during division, highly condensed chromosomes. Each metaphase chromosome has two sister chromatids joined at a centromere. Loosely packed euchromatin is active; tightly packed heterochromatin is mostly inactive.
- Nucleotides are the monomers of nucleic acids: a pentose sugar (deoxyribose in DNA, ribose in RNA), a phosphate group and a nitrogenous base. Purines (two rings): adenine (A) and guanine (G); pyrimidines (one ring): cytosine (C), thymine (T) in DNA and uracil (U) in RNA. Nucleotides join by phosphodiester bonds (condensation) between the 3′ carbon of one sugar and the 5′ phosphate of the next, forming a sugar-phosphate backbone.
- Watson and Crick (1953) model, using Rosalind Franklin's X-ray images and Chargaff's rules (A = T and G = C): DNA is a double helix of two antiparallel strands (5′→3′ and 3′→5′); bases pair by complementary base pairing with hydrogen bonds: A–T (2 H-bonds), G–C (3 H-bonds); one complete turn is 3.4 nm with 10 base pairs.
- RNA is usually single-stranded, contains ribose and uracil, and is shorter. Types: mRNA (carries the code from DNA to ribosomes), tRNA (cloverleaf shape; carries amino acids; has an anticodon), rRNA (with proteins forms ribosomes). DNA is more stable and stores information; RNA is temporary and used in protein synthesis.
- A gene is a sequence of DNA nucleotides that codes for a polypeptide (or functional RNA). Its position on a chromosome is its locus. Eukaryotic genes contain coding exons and non-coding introns. Much of the genome is non-coding (regulatory sequences, repeats).
- The genetic code is a triplet code: three bases (a codon) code for one amino acid. It is universal (same in almost all organisms), degenerate (most amino acids have more than one codon; 64 codons for 20 amino acids), non-overlapping, read from a start codon (AUG) to a stop codon (UAA, UAG, UGA).
- Semi-conservative replication: each new DNA molecule contains one original (parental) strand and one new strand. Meselson and Stahl (1958) proved this by growing bacteria in heavy nitrogen (¹⁵N), then light (¹⁴N): after one generation DNA was all intermediate density; after two, half intermediate and half light.
- Replication steps: (1) DNA helicase unwinds the helix and breaks hydrogen bonds at the replication fork; single-strand binding proteins keep strands apart; topoisomerase (gyrase) relieves twisting. (2) Primase adds a short RNA primer. (3) DNA polymerase adds free nucleotides by complementary base pairing, only in the 5′→3′ direction: the leading strand is made continuously; the lagging strand is made in short Okazaki fragments. (4) Primers are replaced by DNA and DNA ligase joins the fragments with phosphodiester bonds. DNA polymerase also proofreads.
- Telomeres are repeated sequences (TTAGGG in humans) at chromosome ends. Because the lagging strand cannot be completed at the very end, chromosomes shorten each division; telomeres protect genes from being lost. Telomerase (active in stem cells, germ cells and many cancer cells) rebuilds them; telomere shortening is linked to ageing.
- Significance of replication: identical genetic material is passed to daughter cells in mitosis (growth, repair, asexual reproduction) and gametes carry exact genes; proofreading keeps mutations rare, but errors that remain are a source of variation.
Common misconceptions
- "DNA strands run in the same direction." No: the two strands are antiparallel (one 5′→3′, the other 3′→5′).
- "DNA replication is conservative: one molecule is all old and the other all new." No: replication is semi-conservative: each molecule has one old and one new strand.
- "DNA polymerase can add nucleotides in both directions." No: it adds only to the 3′ end (synthesis 5′→3′), hence Okazaki fragments.
- "Uracil pairs with adenine in DNA." No: uracil is found in RNA; in DNA adenine pairs with thymine.
Worked examples
Example 1. A DNA sample contains 30% adenine. Calculate the percentages of thymine, guanine and cytosine.
Solution
By Chargaff's rule, A = T, so T = 30%. A + T = 60%, leaving 40% for G + C. G = C, so G = 20% and C = 20%.
Example 2. Explain the results of Meselson and Stahl's experiment after one and two generations in ¹⁴N.
Solution
Starting DNA was all heavy (¹⁵N). After one generation all DNA was of intermediate density: each molecule had one heavy (old) and one light (new) strand, which rules out conservative replication. After two generations, half was intermediate and half light, exactly as predicted by semi-conservative replication.
Practice questions
Describe the structure of a DNA nucleotide and how nucleotides are joined.
Show answer
A nucleotide has deoxyribose, a phosphate group and a base (A, T, G or C). Condensation forms a phosphodiester bond between the phosphate of one nucleotide and the 3′ carbon of the next sugar, giving a sugar-phosphate backbone.
Common mistake: Saying nucleotides join by hydrogen bonds.
State four features of the Watson-Crick model of DNA.
Show answer
Double helix; two antiparallel strands; sugar-phosphate backbone outside, bases inside; complementary base pairing (A–T, G–C) by hydrogen bonds; 10 base pairs per turn of 3.4 nm.
Common mistake: Saying the strands are parallel.
Give four differences between DNA and RNA.
Show answer
DNA: deoxyribose, thymine, double-stranded, long, stable, in nucleus (mainly). RNA: ribose, uracil, single-stranded, shorter, less stable, in nucleus and cytoplasm; three types (mRNA, tRNA, rRNA).
Common mistake: Saying RNA contains thymine.
Describe how DNA is packaged in eukaryotic chromosomes.
Show answer
DNA wraps around histone octamers to form nucleosomes; these coil into a 30 nm fibre; fibres form loops attached to a protein scaffold; further coiling produces condensed chromosomes visible in mitosis.
Common mistake: Leaving out histones.
Describe the role of each enzyme in DNA replication: helicase, primase, DNA polymerase, ligase.
Show answer
Helicase: unwinds DNA and breaks hydrogen bonds. Primase: makes RNA primers. DNA polymerase: adds complementary nucleotides 5′→3′ and proofreads. Ligase: joins Okazaki fragments by phosphodiester bonds.
Common mistake: Saying ligase unwinds DNA.
Explain what is meant by semi-conservative replication.
Show answer
Each new DNA molecule consists of one original strand that acted as a template and one newly synthesised strand.
Common mistake: Saying both strands are new.
State four properties of the genetic code.
Show answer
Triplet (codon of three bases); universal; degenerate (more than one codon for most amino acids); non-overlapping; has start (AUG) and stop codons.
Common mistake: Saying the code is overlapping.
Explain the significance of telomeres.
Show answer
They are repeated non-coding sequences at chromosome ends that protect genes from loss as ends shorten during replication; their shortening limits cell divisions and is linked to ageing; telomerase rebuilds them in stem and cancer cells.
Common mistake: Confusing telomeres with centromeres.
Matching and drag-and-drop
Matching
Match each item in column A with the correct answer in column B. Write the letter next to each number.
Column A Column B 1. The number of hydrogen bonds between G and C is: a. histones 2. The sugar in DNA is: b. thymine 3. DNA in chromosomes is wound around proteins called: c. three 4. In DNA, adenine pairs with: d. deoxyribose Show answer
1 → c (three) · 2 → d (deoxyribose) · 3 → a (histones) · 4 → b (thymine)
- G–C pairs are stronger.
- RNA contains ribose.
- They form nucleosomes.
- By two hydrogen bonds.
Drag and drop
Choose the correct word or phrase from the box for each gap. One word in the box is not needed.
identical in sequence · telomeres · codon (triplet) · antiparallel- Repeated sequences at the ends of chromosomes are .
- Three bases that code for one amino acid form a .
- The two strands of DNA are described as .
Show answer
1: telomeres · 2: codon (triplet) · 3: antiparallel
- They protect genes during replication.
- The code is a triplet code.
- One runs 5′→3′, the other 3′→5′.
Matching
Match each item in column A with the correct answer in column B. Write the letter next to each number.
Column A Column B 1. The start codon is: a. DNA helicase 2. Chargaff's rules state that in DNA: b. AUG 3. The enzyme that unwinds DNA during replication is: c. purines 4. Adenine and guanine are: d. A = T and G = C Show answer
1 → b (AUG) · 2 → d (A = T and G = C) · 3 → a (DNA helicase) · 4 → c (purines)
- It codes for methionine.
- Due to complementary pairing.
- It breaks hydrogen bonds.
- They have two rings.
Drag and drop
Choose the correct word or phrase from the box for each gap. One word in the box is not needed.
introns · Meselson and Stahl · 32% · 18%- Non-coding sequences within eukaryotic genes are .
- A DNA sample contains 18% cytosine. The percentage of adenine is .
- Semi-conservative replication was proved by .
Show answer
1: introns · 2: 32% · 3: Meselson and Stahl
- They are removed from pre-mRNA.
- G = 18%, so A + T = 64%, A = 32%.
- Using heavy and light nitrogen.