IBDP Biology 2025 SL&HL: D1.2 Protein synthesis Study Notes

Translation: From mRNA to polypeptide

There are many types of RNAs
tRNA = transfer RNA
rRNA = Ribosomal RNA
mRNA = Messenger RNA
etc…
ONLY mRNA are used in translation

Goal of translation ?

Use the information in mRNA to make protein = Translate the sequence in mRNA to know the sequence of protein that has to be made

Why the word “Translation” ?

From one language to a different language
From “mRNA language” to “protein language”
ACUGAUCGGGCUAGCUAGC ………… M P V A T W G

mRNA alphabet is composed of FOUR letters, ACGU = Nucleotides
Protein alphabet is composed of 20 “letters”, ARNDCQEGHILKMFPSTWYW = Amino acids

Three ways to write amino acids

alanine – ala – A    arginine – arg – R    asparagine – asn – N
aspartic acid – asp – D    cysteine – cys – C    glutamine – gln – Q
glutamic acid – glu – E    glycine – gly – G    histidine – his – H
isoleucine – ile – I    leucine – leu – L    lysine – lys – K
methionine – met – M    phenylalanine – phe – F    proline – pro – P
serine – ser – S    threonine – thr – T    tryptophan – trp – W
tyrosine – tyr – Y   valine – val – V

How to know which amino acid is needed
Out of 20 possibilities
When we can only use nucleotides
Out of only 4 nucleotides ???GE

We need a CODE
The Genetic code

Genetic code

Four different bases are used to be translated into a combination of 20 different amino acids
Need for 20 different combinations of bases . There are 4 different bases

One combination of three bases = one mRNA codon

How to use the genetic code?

1. Read the mRNA sequence codon by codon
2. Find the corresponding amino acid
Codon UUU …… amino acid Phe (Phenylalanine)
Codon GAU …… amino acid Asp (Aspartic acid)
Codon AUG …… amino acid Met or Start
(methionine or ???)
Codon UAA …… Stop (???)
Codon UGA …… Stop (???)
Codon UAG …… Stop (???)

The mRNA is read “3 bases at the time”
Three mRNA bases = one codon/triplet
One codon always codes for the same amino acid
The genetic code is non-overlapping
The genetic code is degenerate
The genetic code contains punctuation codons
The genetic code is (almost) universal

• The genetic code is non-overlapping

In a mRNA molecule, codons are consecutive
They are read one by one, one after the other, in a continuous manner
A base is never part of two different codons

• The genetic code is degenerate

One amino acid may be encoded by more than one codon

The genetic code requires at least 20 codons minimum
It contains 64 codons
Contains more information than required
While Methionine and Tryptophane are encoded by single codons
All other amino acids are encoded by more than one codon
“Degeneracy” = the third base of the codon looks less important than
the first and second bases
e.g. Phenylalanine encoded by UUU and UUC
e.g. Proline encoded by CCU, CCC, CCA and CCG

• The genetic code contains punctuation codons

The Start/Methionine codon

The codon AUG encodes the amino acid Methionine
AND
The codon AUG marks the position where translation starts
CONFUSION ?
What if a mRNA contains several AUG codons ?
Start translation at each AUG?
Multiple proteins out of one single mRNA?
Only the first AUG is THE start codon
Any other AUG is used for Methionine
All proteins have Methionine as their first amino acid

The 3 stop codons

Three codons do not encode any amino acids UAA UAG UGA
If they are “read” by the ribosome, translation will end
They do not attract any tRNA+amino acid
They attract a release factor = a protein that can fit in the ribosome where new tRNA+amino acid enter the ribosome
Presence of release factor in ribosome ends translation
The last amino acid is encoded by the codon just before the stop codon

How many amino acids in the polypeptide?

• The genetic code is (almost) universal

(almost)* all organisms use the same genetic code

A human mRNA is translated into the corresponding protein
In a cat’s cell, this human mRNA is translated into the same protein
In a carrot’s cell, this human mRNA is translated into the same protein
In a yeast’s cell, this human mRNA is translated into the same protein
The genetic code is the same in those species
The genetic code is universal

REALLY?

Codon UGA in human’s mRNA: Stop codon
Codon UGA in Mitochondria’s mRNA: Trp (Tryptophane)
Codon UGA in Paramecium’s mRNA: Gln (Glutamine)
The same codon can be read different ways
Different genetic codes
Not all species/organelles use the same genetic code
The genetic code is NOT universal
It is almost universal

Many organisms use the same genetic code
Except some … exceptions
Consequence: Transgenic organisms are possible

Gene A from organism A encoding protein A
Transferred into organism B = genetic transformation
Organism B is now transgenic for gene A from organism A
Organism B will produce protein A from gene A

Jellyfish is green fluorescent
Due to GFP protein
Green Fluorescent Protein

Ribosomes 

Ribosome = Site of translation

Bacteria, mitochondria, chloroplasts

– “smaller”
20 nm diameter

Eukaryotes

– “bigger”
25-30 nm diameter

tRNA = intermediate between mRNA and amino acids

tRNA + amino acid = aminoacyl-tRNA

tRNA = intermediate between mRNA and amino acids

tRNA-activating enzymes ensure the right amino acid is linked to the right RNA

An anticodon is complementary to a codon

One amino acid can be encoded by
One codon (TRP) or More than one codon (LEU – 6 codons)

One amino acid will be attached to
One tRNA – one anticodon (TRP) Or More than one tRNA – more than one anticodon (LEU – 6 tRNAs – 6 anticodons)

Small sub-unit of ribosome binds mRNA
First tRNA-amino acid binds start codon
Complementarity anticodon – codon
Large sub-unit of ribosome binds
Second tRNA-amino acid binds second codon
Complementarity anticodon – codon
Peptide bond made between first and second amino acid
By enzymes in ribosome
Third tRNA-amino acid binds third codon
Complementarity anticodon – codon
Not shown here:
Peptide bond made between first and second amino acid
By enzymes in ribosome
And so on until the stop codon on the mRNA