DNA and Protein SynthesisOxford AQA IGCSE Biology: Revision notes
Section 1
What is the structure of DNA?
DNA is a double helix molecule made up of repeating units called nucleotides. Each nucleotide contains three components:
- A sugar (deoxyribose)
- A phosphate group
- One of four nitrogenous bases: adenine (A), thymine (T), cytosine (C), or guanine (G)
The nucleotides link together to form two long strands that twist around each other in a helical shape. The sugar and phosphate groups form the backbone of each strand, while the bases point inwards towards the centre of the helix.
Examiners expect you to name all three components of a nucleotide when describing DNA structure. Saying 'sugar, phosphate and base' shows clear understanding of the specification.
Think of DNA like a twisted ladder: the sugar-phosphate backbones are the side rails, and the base pairs are the rungs connecting them.
Section 2
How do bases pair together in DNA?
DNA strands are held together by complementary base pairing rules:
| Base on strand 1 | Base on strand 2 |
|---|---|
| Adenine (A) | Thymine (T) |
| Thymine (T) | Adenine (A) |
| Cytosine (C) | Guanine (G) |
| Guanine (G) | Cytosine (C) |
These bases pair through hydrogen bonds, which are relatively weak chemical bonds that can be broken and remade. The specificity of base pairing (A always with T, C always with G) ensures that the two strands are complementary to each other. This means if you know the sequence of bases on one strand, you can predict the sequence on the other strand.
When asked about base pairing, always specify which bases pair together (A-T and C-G). Simply saying 'bases pair' is not enough for full marks.
Students often confuse the number of hydrogen bonds: A-T pairs have 2 hydrogen bonds, while C-G pairs have 3. This detail is sometimes tested but not always required at IGCSE level.
Section 3
How does DNA replicate semi-conservatively? (HT)
Semi-conservative replication is the process by which DNA copies itself. The process occurs in several stages:
- The hydrogen bonds between complementary bases break, causing the double helix to unwind and the two strands to separate
- Each original strand acts as a template for a new strand
- Free nucleotides in the cell bond to the exposed bases following the rules of complementary base pairing (A with T, C with G)
- The enzyme DNA polymerase catalyses the bonding of nucleotides to form the new strands
- Two identical DNA molecules are produced, each consisting of one original strand and one new strand
This is called 'semi-conservative' because each new DNA molecule conserves (keeps) one of the original strands. This ensures accurate copying of genetic information and is essential for cell division and growth.
To gain full marks, explain that each resulting DNA molecule has one original strand and one newly synthesised strand. This demonstrates understanding of why it's called 'semi-conservative'.
If the original DNA strand is 5'-ATCG-3', the new complementary strand will be 5'-CGAT-3'. After replication, you have two identical DNA molecules: one with the original 5'-ATCG-3' strand and a new 5'-CGAT-3' strand, and another with the original strand as template and an identical new copy.
Section 4
How does protein synthesis occur? (HT)
Protein synthesis involves two main processes:
Transcription (DNA → mRNA)
- mRNA polymerase (also called RNA polymerase) binds to the DNA at a specific gene
- The double helix unwinds and the two strands separate
- The mRNA polymerase reads one strand (the template strand) in the 3' to 5' direction
- Free RNA nucleotides are added to form a strand of messenger RNA (mRNA) that is complementary and antiparallel to the template strand
- The mRNA is released and moves out of the nucleus
Note: In mRNA, uracil (U) replaces thymine (T)
Translation (mRNA → protein at ribosomes)
- mRNA binds to a ribosome in the cytoplasm
- The ribosome reads the mRNA in groups of three bases called codons
- Transfer RNA (tRNA) molecules carry specific amino acids to the ribosome
- Each tRNA has an anticodon that is complementary to a codon on the mRNA
- The amino acids are linked together by peptide bonds to form a polypeptide chain (protein)
- Translation continues until a stop codon is reached
Together, transcription and translation convert the genetic code in DNA into a functional protein.
Examiners want to see that you understand transcription happens in the nucleus and translation happens in the cytoplasm. Always state the location when describing each process for full credit.
If a DNA codon sequence is 5'-TAC-3', the mRNA codon produced will be 5'-AUG-3' (note the U replaces T). The tRNA anticodon will be 3'-UAC-5', which is complementary and antiparallel to the mRNA codon.
Section 5
How does the DNA base sequence code for amino acid sequences? (HT)
The genetic code is the system by which triplet sequences of bases (codons) in mRNA determine which amino acids are incorporated into a protein.
The relationship between DNA and protein:
- Each codon (3 bases on mRNA) codes for one amino acid
- Different codons code for different amino acids
- The sequence of codons on mRNA determines the sequence of amino acids in the protein
- The DNA sequence is transcribed into an mRNA sequence, which is then translated into a protein sequence
Key principles:
- The genetic code is degenerate: more than one codon can code for the same amino acid
- The genetic code is universal: almost all organisms use the same genetic code
- The code is read in a continuous sequence from a start codon (AUG) to a stop codon (UAA, UAG, or UGA)
- Any change in the DNA base sequence will result in a change in the mRNA codon sequence, which may change the amino acid sequence and therefore the protein structure and function
Example: DNA: 5'-TAC GTG GTA-3' → mRNA: 5'-AUG CAC CAU-3' → Amino acids: Methionine-Histidine-Histidine
When explaining the genetic code, clearly state that each codon (three bases) codes for one amino acid. Show the progression: DNA sequence → mRNA sequence → amino acid sequence to demonstrate full understanding.
Section 6
What are mutations and how do they occur?
A mutation is a permanent change in the base sequence (DNA sequence) of an organism's DNA. Mutations can have various effects on proteins and organisms.
How mutations affect protein structure and function:
- A change in one base may change the codon
- A changed codon may code for a different amino acid, resulting in a different protein structure
- A different protein structure may have different or non-functional properties
- Some mutations are silent (no amino acid change) if the new codon codes for the same amino acid (due to the degenerate code)
- Mutations affecting early codons may have more severe effects than those near the end
Causes of mutations:
Ionising radiation (e.g. X-rays, gamma rays, UV radiation) can damage DNA by:
- Breaking chemical bonds
- Causing incorrect base pairing during replication
- Triggering cell repair mechanisms that introduce errors
Chemical mutagens (e.g. benzene, formaldehyde, certain pesticides) can:
- Bind to DNA and alter base structure
- Interfere with DNA replication
- Cause breakage of DNA strands
Other causes include errors during DNA replication and exposure to biological agents. The risk of mutation increases with repeated or prolonged exposure to mutagens.
Examiners expect you to explain the chain of events: mutation in DNA → change in mRNA codon → change in amino acid → change in protein structure → change in protein function. Show all steps for full marks.
Students often state that all mutations are harmful. In fact, mutations can be beneficial, harmful, or have no effect (silent mutations). Only explain the consequences based on what the mutation actually does to the protein.
Must Know
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DNA structure: Double helix made of nucleotides containing deoxyribose sugar, phosphate group, and one of four bases (A, T, C, G). Sugar-phosphate forms the backbone; bases point inwards.
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Complementary base pairing: A pairs with T, and C pairs with G. These bases are held together by hydrogen bonds between the two strands.
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Semi-conservative DNA replication: The double helix unwinds, each original strand serves as a template, free nucleotides bond to bases (following complementary base pairing rules), DNA polymerase catalyses bonding, producing two identical DNA molecules each with one original strand and one new strand.
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Transcription and translation: Transcription (in nucleus) copies DNA into mRNA using mRNA polymerase; translation (at ribosomes in cytoplasm) reads mRNA codons and assembles amino acids into proteins using tRNA molecules. Each codon (3 bases) codes for one amino acid.
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Genetic code relationship: The sequence of bases in DNA determines the sequence of codons in mRNA, which determines the sequence of amino acids in the protein. The code is degenerate (multiple codons per amino acid) and universal (used by nearly all organisms).
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Mutations: Permanent changes in DNA base sequence caused by ionising radiation (X-rays, gamma rays, UV) or chemical mutagens (benzene, formaldehyde). A mutation may change a codon, produce a different amino acid, alter protein structure, and affect protein function. Some mutations are silent if the new codon codes for the same amino acid.
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Carry on to the next subtopic.