How DNA codes for proteins
In this IBDP Biology topic, you will understand the formation of protein.
- A gene is a length of DNA that codes for one (or more) polypeptides.
- In the human genome, there are about 25000 genes.
- Each gene occupies a specific locus on a chromosome.
- Genes code for enzymes, they are involved in the control of all metabolic pathways and thus in synthesis of all non-protein molecules found in the cells.

The Genetic Code
- It is a triplet code ( a sequence of three nucleotide bases) for an amino acid.
- It is a degenerate code (all amino acids have more than one code.)
- Some codes don’t correspond to an amino acid, but indicate ‘stop’,
- It is widespread, but not universal.

How the nucleotide sequence code for the amino acid sequence in a polypeptide?
Transcription ( the first stage of protein synthesis )
- To be transcribed, a gene has to unwind and unzip (hydrogen bonds between bases break as the gene dips into the nucleolus).
- Activated RNA nucleotides bind to complementary bases on the template strand (catalysed by the enzyme RNA polymerase).
- The two extra phosphates are released, releasing energy for bonding adjacent nucleotides.
- The mRNA produced is complementary to that on the template strand and is therefore a copy of the base sequence on the coding strand of the length of the DNA.
- The mRNA is released from the DNA and passes out of the nucleus, through a nuclear pore, to a ribosome.

Translation (the assembly of polypeptides at ribosomes)
- The second stage of protein synthesis, when the amino acids are assembled into a polypeptide.
- They are assembled into the sequence dictated by the sequence of codons on the mRNA.
- The genetic code, copied from DNA to mRNA, is now translated into a sequence of amino acids. This is a polypeptide.
- It happens in ribosomes, which may be free in the cytoplasm but many are bound to the rough endoplasmic reticulum.

Ribosomes
- Assembled in the nucleolus of eukaryote cells, from ribosomal RNA and protein.
- There is a groove in which the length of mRNA can fit. The ribosome then moves along he mRNA, reading the code and assembling the amino acids.
The sequence of amino acids;
- forms the primary structure of a protein
- primary structure determines the tertiary structure, allowing it to fold up into the 3d shape.
- tertiary structure is what allows a protein to function.
Transfer RNA
- Another form of RNA, tRNA is made in the nucleus and passes into the cytoplasm.
- They are lengths of RNA folded into hairpin shape, with three exposed bases where a particular amino acid can bind.
- At the other end there are three unpaired nucleotide base, known as an anticodon. Each anticodon can bind temporarily with its complementary codon.

How the polypeptide is assembled
- A molecule of mRNA binds to a ribosome. Two codons are attached to a small subunit of the ribosome and exposed to the large subunit. The first exposed mRNA codon is always AUG. Using ATP energy and an enzyme, a tRNA with methionine and the anticodon UAC forms hydrogen bonds with this codon.
- A second tRNA, bearing a different amino acid, binds to the second exposed codon with its complementary anticodon.
- A peptide bond forms between the two adjacent amino acids. An enzyme, present in the small ribosomal subunit, catalyses the reaction.
- The ribosome now moves along the mRNA, reading the next codon. A third tRNA brings another amino acid, and a peptide bond forms between it and the dipeptide. The first tRNA leaves and is able to collect and bring another of its amino acids.
- The polypeptide chain grows until a stop codon is reached. There are no corresponding tRNAs for those three codons, UAA, UAC or UGA, so the polypeptide chain is now complete.

Mutations
A mutation is a change in the amount of, or arrangement of, the genetic material in a cell.
Chromosome mutation involves changes to parts of or whole chromosomes.
DNA mutations are changes to genes due to changes in nucleotide base sequences;
- Point mutations in which one base pair replaces enough (sustitutions)
- Insertion/deletion mutations in which one or more nucleotide pairs are inserted or deleted from a length of DNA (framshift)

Mutations with neutral effects
If a gene is altered by change to its bases sequences, it becomes another version of the same gene, it is an allele of the gene. It may produce no change if;
- The mutation is in a non-coding region of the DNA
- It is a silent mutation. Although the base triplet has changed, it still codes for the same amino acid, so the protein is unchanged.
If the mutation does cause a change of characteristics, but this characteristic gives no effect to the organism, it is also thought as neutral.
Mutations with harmful or beneficial effects
- Early humans in Africa most certainly had dark skin.
- The pigment protected them from the harmful effects of UV light, but they could still synthesis vitamin D from the sunlight on their skin.
- Any humans who had mutations to some of the genes determining skin color, producing paler skin would have been burnt.
- As humans migrated to more temperate climates, the sunlight was not as intense enough to make vitamin D on dark skins.
- Humans with the mutation would have been able to synthesis more vitamin D.
- The environment is never static, and when it changes, people who have a certain characteristic may be better adapted to the new environment.
This is the end of the topic

Drafted by Eva (Biology)
Photo references:
- https://medlineplus.gov/genetics/understanding/basics/gene/
- https://sejkai.gitbook.io/academic/biology/central_dogma
- https://courses.lumenlearning.com/wm-biology1/chapter/reading-steps-of-genetic-transcription/
- https://www.youtube.com/watch?v=7R-fxGmqw-0
- https://en.wikipedia.org/wiki/Transfer_RNA
- https://ib.bioninja.com.au/standard-level/topic-2-molecular-biology/24-proteins/gene--polypeptide.html
- https://ib.bioninja.com.au/standard-level/topic-3-genetics/32-chromosomes/block-mutations.html