DNA & Protein Synthesis


DNA is possibly the single most important molecule in the body. Its double helix has come to represent one of the most important discoveries made in the field of biology.

Structure of DNA

Specification Reference

"Know the structure of DNA, including the structure of the nucleotides (purine's and pyrimidine's), base pairing, the two sugar-phosphate back bones, phosphodiester bonds and hydrogen bonds."
DNA is made up of nucleic acid. Each nucleotide is made up of the following three parts:
  • A nitrogen containing base
  • A pentose sugar
  • A phosphate-group
In DNA the sugar is deoxyribose whereas in RNA the sugar is ribose. There are also two different types of bases:
  • Purine base - has two rings
  • Pyrimidine base - has one ring
Purines Pyrimidines
Adenine (A) Cytosine (C)
Guanine (G) Thymine (T)
Uracil (U)
Each pair must have three rings and they are joined together by hydrogen bonds. Therefore each bond must involve hydrogen. Because of these rules each base will only join with another if they are complementary. The following bases are complementary:
  • A & T
  • G & C

Making Polynucleotides

Nucleic acids are chains or nucleotides joined together to form a polynucleotide. The bonds between each nucleotide form in a condensation reaction between the OH from a phosphate group and OH from the ribose sugar. This results in the formation of a phosphodiester bond and in turn the sugar-phosphate backbone.
  • RNA molecules form single strands and can fold into complex shapes.
  • DNA molecules form two stands which twist around each other to form a double helix.

DNA Replication

Specification Reference

"Understand how DNA is replicated semi-conservatively, including the role of DNA helicase, polymerase and ligase."
After the double helix was discovered it took many years before scientists discovered how DNA replicated. The following suggestions were made:
  • Conservative
  • Semi-conservative
  • Dispersive
To solve this problem Meseleson and Stahl carried out an experiment using different isotopes of nitrogen and where able to determine that DNA replicated semi-conservatively as shown below:
  1. A double helix of DNA is taken.
  2. The chains of nucleotides fit perfectly together as long as the base pairs are matched correctly.
  3. When the DNA replicates, the two strands if the DNA molecule "unzip" as DNA Helicase breaks the hydrogen bonds between each of the base pairs. This results in two separate strands which can now act as templates for new DNA molecules.
  4. The new template stands have exposed bases which now attract free DNA nucleotides and new hydrogen bonds are formed between the matching base pairs. DNA Polymerase lines up the nucleotides and catalyses the formation of phosphodiester bonds. DNA Ligase then joins sections of DNA together to form a new strand.
  5. The result is two new molecules of DNA, each containing one original and one new strand. This is called semi-conservative replication.

The Genetic Code

Specification Reference

"Understand the nature of the genetic code, including triplets coding for amino acids, start and stop codons, degenerate and non-overlapping nature, and that not all the genome codes for proteins."
A gene is simply a sequence of bases on a DNA molecule coding for a sequence of amino acids in a polypetide chain. The genetic code has number of properties that allow life to exist as we know it. These features are detailed below:
  • The Triplet Code - each set of three bases codes for one amino acid resulting in 64 possible combinations (4x4x4).
  • Degenerate - this means that each amino acid is coded for by more than one triplet (the word codon can also be used to describe a triplet).
  • Non-overlapping - this means that each triplet is separate and one base can only be part of one triplet.
Having a degenerate genetic code is a big advantage to life. This is because point mutations will not always change the amino acid that is coded for meaning the protein will still be produced as intended. For example, leucine is coded for by AAT and AAC. A mutation, changing the last base in the triplet will not always alter the amino acid that is coded for resulting in no negative effects on the organism.

Messenger RNA (mRNA)

Specification Reference

"Know the structure of mRNA including nucleotides, the sugar phosphate backbone and the role of hydrogen bonds."
mRNA is formed in the nucleus and usually contains instructions for one polypeptide chain. Messenger RNA codes on the antisense strand. This means that when the molecule is translated at the ribosomes, the new strand will become sense. mRNA is formed through the following process:
  • A section of the DNA molecule is unraveled and is transcribed onto strands of mRNA by RNA Polymerase.
  • The RNA polymerase catalyses the formation of phosphodiester bonds between the phosphate, the sugar and the bases.
  • Complementary bases line up alongside the DNA and join up with the mRNA strand.
  • The mRNA will then exit the nucleus through a pore and enter the cytoplasm.

Transfer RNA (tRNA)

Specification Reference

"Know the structure of tRNA, including nucleotides, the role of hydrogen bonds and the anticodon."
tRNA is found in the cytoplasm and has a complex shape, similar to that of a four leaf clover. The properties of tRNA are listed below:
  • Each molecule of tRNA contains a sequence of three bases known as the anticodon.
  • The three bases in this anticodon will determine which amino acid the tRNA molecule joins to and its binding site (in other word the anticodon is specific to the amino acid it is carrying).
  • The tRNA molecule will then carry this specific amino acid into position at the ribosomes as it lines up with a complementary codon on strand of mRNA.
  • It is here at the surface of the ribosomes that the process of translation will occur.

Transcription & Translation

Specification Reference

"Understand the processes of transcription in the nucleus and translation at the ribosome, including the role of sense and anti-sense DNA, mRNA, tRNA and the ribosomes."
Transcription and translation are two key processes involved in proteins synthesis that are outlined below:

Transcription

  1. RNA polymerase attaches to the start of the gene and the DNA "unwinds".
  2. Free bases are attracted to the antisense strand of the DNA.
  3. RNA polymerase moves along the strand forming phosphodiester bonds between nucleotides.
  4. This form a strand of mRNA which then exits the nucleus through a nuclear pore.

Translation

  1. mRNA enters the cytoplasm and attaches itself to a ribosome.
  2. tRNA molecules line up to the codon complementary to its anticodon.
  3. The tRNA anticodon is specific to the amino acid that it is carrying.
  4. Enzymes link the amino acids together to form a polypeptide chain.
  5. Hydrogen bonds hold the tRNA and mRNA in place while this occurs.
  6. The ribosome will then continue to move down strand of mRNA adding more amino acids to the polypeptide chain until it reaches a STOP codon.

Gene Mutations

Specification Reference

"Understand the term gene mutation as illustrated by base deletions, insertions and substitutions."
A gene mutation is a permeant change in the sequence of bases in an organism. There are three different types of mutations, as shown below:
  • Substitution - when one base is added and another is removed. This usually has a small impact since it only affects one triplet.
  • Deletion - when one base is removed, causing all of the following bases to move by one position. This is known as a frame shift and can have serious consequences.
  • Insertion - occurs when one base is added, again causing all of the bases to shift by one position. This is also known as a frame shift.

Sickle Cell Anaemia

Specification Reference

"Understand the effect of point mutations on amino acid sequences, as illustrated by sickle cell anaemia in humans."
This is a genetic condition caused by a point mutation, resulting in a potentially fatal condition.
  1. Point mutation substitutes a T to A
  2. This results in the wrong amino acid being coded for
  3. Resulting in a faulty polypeptide chain
  4. This reduces the solubility of haemoglobin when deprived of oxygen
  5. This causes it to precipitate out of the blood
  6. The red blood cells become deformed into a sickle shape
  7. This new shape restrict their movement through capillaries
  8. So the body removes these cells resulting in anaemia
However, the malaria parasite cannot infect these sickle shaped red blood cells. This makes it advantageous to have the point mutation in areas with high levels of malaria infection.