D. Molecular Genetics · Molecular GeneticsThe Structure of DNA and RNA
D3.2 D2.1 D2.2 A1.12About 70 minutes
Learning goals- I can draw a nucleotide and label the phosphate, the sugar (with carbons 1′ to 5′) and the nitrogenous base.
- I can explain how phosphodiester bonds, complementary base pairing and antiparallel strands give DNA its structure.
- I can write the complementary strand of a DNA sequence with correct 5′ and 3′ labels.
- I can compare the structure and functions of DNA and RNA, including the three main kinds of RNA.
- I can describe how DNA is packaged in prokaryotic and eukaryotic cells.
Words to know
nucleotide
The monomer of nucleic acids: a phosphate group, a five-carbon sugar and a nitrogenous base.
deoxyribose
The five-carbon sugar in DNA. It has an H instead of an OH on carbon 2′.
purine
A double-ring nitrogenous base: adenine (A) and guanine (G).
pyrimidine
A single-ring nitrogenous base: cytosine (C), thymine (T) and, in RNA, uracil (U).
phosphodiester bond
The covalent link between the 3′ carbon of one nucleotide's sugar and the phosphate on the 5′ carbon of the next, forming the backbone.
antiparallel
Running in opposite directions: one DNA strand runs 5′→3′ and its partner runs 3′→5′.
complementary base pairing
A pairs with T (or U in RNA) by 2 hydrogen bonds, and G pairs with C by 3 hydrogen bonds.
histone
A small, positively charged protein that DNA wraps around in eukaryotic cells.
nucleosome
About 147 base pairs of DNA wrapped around a core of eight histone proteins.
mRNA, tRNA, rRNA
Messenger RNA carries a gene's code to the ribosome; transfer RNA brings amino acids; ribosomal RNA forms the core of the ribosome.
Two metres in a nucleus
The DNA in one of your cells, stretched out, would be about 2 metres long. It has to fit inside a nucleus a few micrometres across, be copied perfectly before every cell division, and still let the cell read any gene it needs within minutes. The structure of DNA explains how all three are possible.
In the last lesson you followed the race to discover the double helix. Now you will learn the structure in the detail you need for replication, transcription and biotechnology. Everything in this unit depends on it, especially the idea of the 5′ and 3′ ends.
The nucleotide
DNA and RNA are nucleic acids: polymers built from monomers called nucleotides. Each nucleotide has three parts:
- A phosphate group (negatively charged).
- A five-carbon sugar (a pentose). The carbons are numbered 1′ to 5′ ("one prime" to "five prime"). The prime marks show they belong to the sugar, not to the base.
- A nitrogenous base attached to carbon 1′.
The phosphate is attached to carbon 5′. Carbon 3′ carries an OH group, and that is where the next nucleotide attaches.
Four bases, two families
The bases come in two families. Purines have two fused rings: adenine (A) and guanine (G). Pyrimidines have one ring: cytosine (C), thymine (T) in DNA, and uracil (U) in RNA.
A memory trick: "Pure As Gold" (purines are A and G) and "CUT the Py" (C, U and T are pyrimidines).
Building a strand: the sugar-phosphate backbone
Nucleotides join by a condensation (dehydration) reaction between the 3′ OH of one sugar and the 5′ phosphate of the next, releasing water. The link is a phosphodiester bond. (You met condensation reactions in the Biochemistry unit.)
The result is a chain with a repeating sugar-phosphate backbone and the bases sticking out to one side. The chain has direction:
- one end has a free phosphate on a 5′ carbon: the 5′ end;
- the other end has a free OH on a 3′ carbon: the 3′ end.
By convention we always write sequences 5′ to 3′, left to right, unless the ends are labelled. And here is a rule you will use all unit: new nucleotides can only be added to the 3′ end of a growing chain.
The double helix
Two strands wind around each other into a right-handed double helix:
- Backbones outside, bases inside. The negatively charged phosphates face the watery cytoplasm; the bases (which are less polar) stack in the middle.
- Complementary base pairing. A pairs with T by 2 hydrogen bonds; G pairs with C by 3 hydrogen bonds. A purine always pairs with a pyrimidine, so every rung is the same width and the helix has a uniform diameter of about 2 nm.
- Antiparallel strands. One strand runs 5′→3′ and the other runs 3′→5′.
- Dimensions. Each base pair adds about 0.34 nm of length, and one full turn is about 3.4 nm, or about 10 base pairs.
- Grooves. Because the sugars attach to the bases at an angle, the helix has a wide major groove and a narrow minor groove. Proteins that switch genes on and off "read" the bases through these grooves without unzipping the DNA.
Hydrogen bonds are weak one at a time, so the strands can be separated by enzymes (or by heat) for copying and reading. But millions of them together, plus the stacking of the bases, make the helix very stable. DNA with more G-C pairs needs a higher temperature to separate, because each G-C pair has one extra hydrogen bond.
Worked exampleExample 1: Writing a complementary strand
One strand of DNA is 5′-ATGCCTGA-3′. Write the complementary strand (a) under it, lined up, and (b) in the standard 5′→3′ form.
- Pair each base: A↔T, T↔A, G↔C, C↔G. Under 5′-A T G C C T G A-3′ write T A C G G A C T.
- The partner strand is antiparallel, so its left end (under the original 5′ end) is its 3′ end: 3′-TACGGACT-5′.
- To write it 5′→3′, read it backwards: 5′-TCAGGCAT-3′.
- Check: reverse the answer to TACGGACT and pair it with the original, base by base: A-T, T-A, G-C, C-G, C-G, T-A, G-C, A-T. ✓
(a) 3′-TACGGACT-5′ (lined up); (b) 5′-TCAGGCAT-3′.
Worked exampleExample 2: How long is the genome?
One set of human chromosomes has about 3.1 × 10⁹ base pairs. How long would this DNA be if stretched out? How long is the DNA in a diploid body cell?
- Each base pair adds 0.34 nm = 0.34 × 10⁻⁹ m.
- Length = 3.1 × 10⁹ × 0.34 × 10⁻⁹ m = 1.05 m (about 1 m).
- A diploid cell has two sets: 2 × 1.05 m ≈ 2.1 m.
About 1 m per set of chromosomes, so about 2 m in a diploid cell.
Packing it in: prokaryotes and eukaryotes
Prokaryotes (bacteria and archaea) usually have one circular chromosome in a region called the nucleoid, with no nuclear membrane. The E. coli chromosome has about 4.6 million base pairs; it is twisted on itself (supercoiled) and held by proteins to fit. Many bacteria also carry small extra circles of DNA called plasmids, which you will use as tools in the biotechnology lessons.
Eukaryotes have several linear chromosomes inside a nucleus. The DNA wraps around histones, small proteins that are positively charged (rich in lysine and arginine) and so attract DNA's negative phosphates. About 147 base pairs wrap around a core of eight histones to form a nucleosome. Under an electron microscope this looks like "beads on a string". Nucleosomes coil and loop into thicker fibres. The DNA-protein complex is called chromatin.
- Loosely packed euchromatin contains genes that are being used.
- Tightly packed heterochromatin is mostly silent.
You will see in the lesson on Controlling Genes in Eukaryotes that the cell switches genes on and off partly by loosening or tightening this packing.
RNA: DNA's working copy
RNA (ribonucleic acid) is also a chain of nucleotides, but with three structural differences:
- The sugar is ribose, with an OH on carbon 2′. That extra OH makes RNA more chemically reactive and much less stable than DNA, which suits a short-lived message.
- Uracil (U) replaces thymine. U pairs with A.
- RNA is usually single-stranded, but it can fold back on itself where bases pair, forming hairpins and complex 3-D shapes.
The three main kinds of RNA in protein synthesis:
- Messenger RNA (mRNA) carries a copy of a gene's code from the DNA to a ribosome.
- Transfer RNA (tRNA) is a small folded RNA that carries one specific amino acid and has an anticodon that pairs with the mRNA.
- Ribosomal RNA (rRNA) combines with proteins to form the ribosome, and rRNA itself catalyzes the joining of amino acids.
Cells also make other RNAs, such as the small RNAs that help splice mRNA and the microRNAs that silence genes. You will meet them later in the unit.
| Feature | DNA | RNA |
|---|
| Sugar | deoxyribose (H on 2′) | ribose (OH on 2′) |
| Bases | A, T, G, C | A, U, G, C |
| Strands | usually double, antiparallel helix | usually single, folds on itself |
| Length | very long (millions of base pairs per chromosome) | short (tens to thousands of nucleotides) |
| Stability | very stable; long-term storage | less stable; short-lived working copy |
| Location in eukaryotes | nucleus (also mitochondria and chloroplasts) | made in nucleus; works mostly in cytoplasm |
| Main job | store and pass on genetic information | carry out the instructions (mRNA, tRNA, rRNA) and regulate genes |
Worked exampleExample 3: DNA, RNA or something else?
A lab analyses four nucleic-acid samples. Decide whether each is double-stranded DNA, single-stranded DNA or RNA.
(a) A 30%, T 30%, G 20%, C 20% (b) A 24%, U 26%, G 31%, C 19% (c) A 22%, T 34%, G 25%, C 19%
- (a) Contains T and no U, so it is DNA. A = T and G = C, which fits double-stranded DNA.
- (b) Contains U, so it is RNA. (A ≠ U and G ≠ C is normal for a single-stranded molecule.)
- (c) Contains T, so it is DNA, but A ≠ T and G ≠ C, so the bases are not paired: single-stranded DNA (as in some viruses).
(a) double-stranded DNA; (b) RNA; (c) single-stranded DNA.
Just for funIf you read your genome aloud at one base per second without ever sleeping, one set of chromosomes (3.1 billion bases) would take about 98 years. And you have two sets.
Hands-on activityBuild an antiparallel DNA model
You need: 2 strips of cardboard or stiff paper (about 30 cm × 3 cm) for backbones, 8 smaller paper strips for bases (4 long ones about 6 cm for purines and 4 short ones about 4 cm for pyrimidines), a pen, tape, and scissors (use them carefully).
- On each backbone strip, draw 4 sugar pentagons evenly spaced. Label the top of the left strip 5′ and its bottom 3′. Label the right strip 3′ at the top and 5′ at the bottom.
- Label the long base strips A, G, A, G and the short ones T, C, T, C.
- Choose the sequence 5′-AGCT-3′ for the left strand. Tape the matching base strip to each sugar on the left strand, pointing inward.
- Now pair each with its partner on the right strand: a long purine must pair with a short pyrimidine. Check that each rung has the same total length (about 10 cm).
- Draw 2 short lines between A and T and 3 between G and C for hydrogen bonds.
- Hold the top and bottom and gently twist to the right to make a helix.
Think about it: Read your right strand from its 5′ end. What sequence is it? (Answer: 5′-AGCT-3′. This sequence is its own reverse complement, a palindrome, which you will meet again with restriction enzymes.) Why would an A-G "rung" not fit? (Two purines would be too wide.)
Your turn
1Name the three parts of a nucleotide and state which sugar carbon each of the other two parts attaches to.
Phosphate (on carbon 5′), five-carbon sugar, and nitrogenous base (on carbon 1′).
2Write the complementary strand of 5′-GGATCCTAAG-3′ in the 5′→3′ direction.
Complement lined up: 3′-CCTAGGATTC-5′. Written 5′→3′: 5′-CTTAGGATCC-3′.
3Why does a purine always pair with a pyrimidine?
A purine (2 rings) plus a pyrimidine (1 ring) gives every rung the same width, so the helix has a uniform 2 nm diameter. Two purines would be too wide; two pyrimidines too narrow.
4Which would separate into single strands at a higher temperature: DNA that is 60% G + C or DNA that is 40% G + C? Explain.
The 60% G + C DNA. G-C pairs have 3 hydrogen bonds (A-T pairs have 2), so more energy is needed to separate the strands.
5Give three structural differences between DNA and RNA.
RNA has ribose (OH on 2′) instead of deoxyribose; uracil instead of thymine; and is usually single-stranded instead of a double helix.
6How many base pairs are in one turn of the double helix, and how long is one turn?
About 10 base pairs per turn, about 3.4 nm long (0.34 nm per base pair).
More practice: warm-up
Adenine (A) and guanine (G).
2How many hydrogen bonds join G and C?
3Which base is found in RNA but not in DNA?
4What kind of bond joins nucleotides in the backbone?
DNA (about 147 base pairs) wrapped around a core of eight histone proteins.
More practice: on your own
1A strand of DNA is written 3′-TTAGCCAT-5′. Write its complementary strand 5′→3′.
Lined up, the complement runs 5′→3′: 5′-AATCGGTA-3′. (No reversing is needed because the partner's left end is already 5′.)
2A double-stranded DNA molecule has 500 base pairs and 140 G-C pairs. How many hydrogen bonds hold the two strands together?
A-T pairs = 500 − 140 = 360. Bonds = 360 × 2 + 140 × 3 = 720 + 420 = 1140 hydrogen bonds.
3Explain why histones bind tightly to DNA.
Histones are rich in positively charged amino acids (lysine, arginine). DNA's phosphate backbone is negatively charged, so opposite charges attract.
4The E. coli chromosome has 4.6 × 10⁶ base pairs. How long is it if stretched out? The cell is about 2 µm long. About how many times longer than the cell is the DNA?
4.6 × 10⁶ × 0.34 nm = 1.56 × 10⁶ nm = 1.56 mm. 1.56 mm ÷ 0.002 mm ≈ 780 times longer.
5Why is it an advantage for mRNA to be less stable than DNA?
mRNA is a temporary message. If it breaks down quickly, the cell can stop making a protein soon after it stops transcribing the gene, so protein levels can change quickly. DNA must last the life of the cell, so it needs to be stable.
Challenge
1Explain, using the structure of the backbone, why DNA strands can only be extended at the 3′ end.
A new nucleotide is joined by a phosphodiester bond between the 3′ OH of the last sugar in the chain and the 5′ phosphate of the incoming nucleotide. The 5′ end of a chain has no free OH to react, so a new nucleotide can only be added at the free 3′ OH. (You will see in DNA replication that this is why one strand is copied in pieces.)
2A segment of double-stranded DNA is 34 nm long. How many base pairs, how many complete turns, and how many nucleotides does it contain?
34 nm ÷ 0.34 nm = 100 base pairs; 100 ÷ 10 = 10 turns; 2 × 100 = 200 nucleotides.
3Scientists find a microbe whose DNA they think may form a triple helix. Using Chargaff's rules and Franklin's data as models, what two kinds of evidence would help test the idea?
(1) Base composition: if strands pair in a particular way, the amounts of certain bases should match in a predictable ratio (as A = T and G = C do for two strands). (2) X-ray diffraction or other structural data: the diameter and repeat distances should fit three strands, and the density (mass per length) should be higher than for a double helix. (Linus Pauling's 1953 triple-helix model failed partly because it put the phosphates inside, which did not fit the data.)
Quiz
1. On which carbon of the sugar is the nitrogenous base attached?
2. The complementary strand of 5′-AGGTCA-3′, written 5′→3′, is:
3. Which statement about DNA strands is correct?
4. Which is true of RNA but not of DNA?
5. Which RNA forms the core of the ribosome and catalyzes peptide bonds?
6. Why do histones bind DNA?
Big ideas (D3.2, D2.1, D2.2): DNA is two antiparallel chains of nucleotides held together by complementary base pairs. Directions (5′ and 3′) matter for everything that follows in this unit: copying, reading and engineering DNA.
How to help: Give your teen a short strand like 5′-GATTACA-3′ and ask for the complementary strand written 5′→3′ (answer: 5′-TGTAATC-3′). Ask them to say why they reversed it.
Common difficulties:
- Forgetting to reverse the complement when writing it 5′→3′ (or reversing when the ends are already labelled).
- Saying the strands are held by covalent bonds. Within a strand: covalent phosphodiester bonds. Between strands: hydrogen bonds.
- Mixing up purines and pyrimidines ("Pure As Gold").
- Thinking RNA is just "single-stranded DNA". It has a different sugar and U instead of T.
The model activity uses scissors; supervise as needed.